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/7787021/working' mkdir: created directory `/scratch/stefan/7787021/working/protonate' Storing results in /scratch/stefan/7787021/finished Working in /scratch/stefan/7787021/working /scratch/stefan/7787021/working /scratch/stefan/7787021 /scratch/stefan/7787021/working/protonate /scratch/stefan/7787021/working /scratch/stefan/7787021 Precomputing protomers for all compounds (pH: 7.4) Dec 03, 2019 8:43:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Dec 03, 2019 8:43:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. ph 7.4: 1062 protomers created Coalesing and merging protomers 1031 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1047 protomers after new stereo-center expansion /scratch/stefan/7787021/working /scratch/stefan/7787021 Bulk generating 3D conformations all protomers in /scratch/stefan/7787021/working/3D mkdir: created directory `/scratch/stefan/7787021/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7787021/working/protonate/xaaabiq-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' 1048 3D conformations generated for 1000 compounds Building REAL300025241150 mkdir: created directory `/scratch/stefan/7787021/working/building' mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241150' /scratch/stefan/7787021/working/building/REAL300025241150 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241150 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241150/0 /scratch/stefan/7787021/working/building/REAL300025241150 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1 `/scratch/stefan/7787021/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=NN1) `REAL300025241150.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241150 none CC1=C(F)C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 7, 7, 15, 15, 42, 67, 151, 151, 151, 151, 151, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 42, 42, 151, 7] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 344 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: REAL300025241150 none CC1=C(F)C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 151, 185, 151, 151, 151, 151, 147, 121, 83, 121, 29, 83, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 151, 151, 151, 151, 151, 151, 151, 147, 147, 121, 121, 121, 29, 29, 1, 201] 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]) total number of confs: 711 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: REAL300025241150 none CC1=C(F)C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 7, 7, 7, 7, 7, 11, 15, 15, 33, 33, 79, 111, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 11, 11, 15, 15, 15, 79, 79, 201, 1] 201 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: 534 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241150 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241150 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `/scratch/stefan/7787021/finished' Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241150/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241150 Building REAL300025241151 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241151' /scratch/stefan/7787021/working/building/REAL300025241151 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241151 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241151/0 /scratch/stefan/7787021/working/building/REAL300025241151 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/2 `/scratch/stefan/7787021/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC12CC(C1)C2)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241151.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241151 none CN(CC1CCCN1C(=O)CC12CC(C1)C2)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 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: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 1, 1, 1, 1, 1, 1, 7, 8, 8, 16, 17, 20, 20, 20, 20, 20, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 16, 16, 20] 20 rigid atoms, others: [45, 43, 40, 41, 10, 11, 12, 13, 14, 15, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49]) total number of confs: 70 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: REAL300025241151 none CN(CC1CCCN1C(=O)CC12CC(C1)C2)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 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: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 9, 9, 7, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 1] 20 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: 68 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: REAL300025241151 none CN(CC1CCCN1C(=O)CC12CC(C1)C2)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 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: [2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 2, 3, 3, 6, 8, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 9] 20 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 50 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241151 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241151 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241151/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241151 Building REAL300025241152 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241152' /scratch/stefan/7787021/working/building/REAL300025241152 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241152 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241152/0 /scratch/stefan/7787021/working/building/REAL300025241152 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/3 `/scratch/stefan/7787021/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC(CC#C)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241152.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241152 none C#CCC(CC#C)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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: [1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 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: [172, 172, 166, 117, 166, 196, 196, 114, 117, 114, 114, 114, 114, 112, 98, 65, 98, 27, 66, 13, 1, 1, 1, 1, 1, 1, 1, 172, 172, 172, 166, 196, 196, 196, 114, 114, 114, 114, 114, 114, 114, 112, 112, 98, 98, 98, 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: 893 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: REAL300025241152 none C#CCC(CC#C)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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: [1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 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: [10, 10, 5, 3, 5, 9, 9, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 22, 35, 114, 114, 114, 114, 114, 10, 10, 10, 5, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 22, 22, 114] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 273 number of broken/clashed sets: 102 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241152 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241152 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241152/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241152 Building REAL300025241153 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241153' /scratch/stefan/7787021/working/building/REAL300025241153 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241153 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241153/0 /scratch/stefan/7787021/working/building/REAL300025241153 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/4 `/scratch/stefan/7787021/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)C(C)O) `REAL300025241153.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241153 none CCC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)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', 'C.3', 'N.am', 'C.3', '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, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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, 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, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 10, 10, 10, 10, 30] 30 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]) total number of confs: 56 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: REAL300025241153 none CCC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)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', 'C.3', 'N.am', 'C.3', '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, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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, 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: [3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 6, 7, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 8, 3, 3, 3, 3, 9] 30 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37] set([0, 1, 2, 4, 11, 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, 51]) total number of confs: 46 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241153 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241153 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241153/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241153 Building REAL300025241154 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241154' /scratch/stefan/7787021/working/building/REAL300025241154 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241154 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241154/0 /scratch/stefan/7787021/working/building/REAL300025241154 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/5 `/scratch/stefan/7787021/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(F)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241154.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241154 none COC(F)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 12, 5, 15, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 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 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 12, 16, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1] 16 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: 52 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: REAL300025241154 none COC(F)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 12, 5, 15, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 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 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 3, 6, 1, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 6, 8, 12, 12, 12, 12, 12, 7, 7, 7, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 12] 16 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 57 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241154 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241154 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241154/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241154 Building REAL300025241155 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241155' /scratch/stefan/7787021/working/building/REAL300025241155 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241155 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241155/0 /scratch/stefan/7787021/working/building/REAL300025241155 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/6 `/scratch/stefan/7787021/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C(C#N)=CC1CC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241155.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241155 none CN(CC1CCCN1C(=O)C(C#N)=CC1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.1', 'N.1', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 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] 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: [10, 10, 9, 9, 9, 9, 9, 9, 4, 9, 4, 4, 4, 1, 1, 1, 1, 10, 11, 11, 13, 16, 21, 21, 21, 21, 21, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 9, 4, 1, 1, 1, 1, 1, 13, 13, 21] 21 rigid atoms, others: [40, 41, 42, 43, 44, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47]) total number of confs: 58 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241155 none CN(CC1CCCN1C(=O)C(C#N)=CC1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.1', 'N.1', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 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] 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: [13, 13, 13, 13, 13, 13, 13, 13, 13, 14, 14, 16, 16, 16, 16, 21, 21, 13, 13, 10, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 16, 21, 21, 21, 21, 21, 13, 13, 1] 21 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: 61 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: REAL300025241155 none CN(CC1CCCN1C(=O)C(C#N)=CC1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.1', 'N.1', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 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] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 9, 9, 3, 4, 4, 6, 8, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 9, 9, 6, 6, 13] 21 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 62 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241155 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241155 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241155/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241155 Building REAL300025241156 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241156' /scratch/stefan/7787021/working/building/REAL300025241156 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241156 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241156/0 /scratch/stefan/7787021/working/building/REAL300025241156 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/7 `/scratch/stefan/7787021/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)ON=C1) `REAL300025241156.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241156 none CCC1=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 4, 4, 10, 10, 31, 52, 158, 158, 158, 158, 158, 5, 5, 5, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 31, 31, 158, 5] 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: 341 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241156 none CCC1=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 184, 184, 161, 158, 161, 158, 158, 158, 158, 153, 120, 82, 120, 27, 82, 13, 1, 1, 1, 1, 1, 1, 1, 184, 184, 184, 201, 201, 201, 201, 201, 158, 158, 158, 158, 158, 158, 158, 153, 153, 120, 120, 120, 27, 27, 1, 184] 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]) total number of confs: 744 number of broken/clashed sets: 77 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241156 none CCC1=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 5, 5, 5, 5, 5, 9, 10, 10, 20, 20, 49, 72, 184, 184, 184, 184, 184, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 9, 9, 10, 10, 10, 49, 49, 184, 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: 412 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241156 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241156 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241156/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241156 Building REAL300025241157 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241157' /scratch/stefan/7787021/working/building/REAL300025241157 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241157 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241157/0 /scratch/stefan/7787021/working/building/REAL300025241157 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/8 `/scratch/stefan/7787021/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CS(N)(=O)=O)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241157.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241157 none CN(CC1CCCN1C(=O)CS(N)(=O)=O)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 8, 11, 11, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 6, 6, 7, 6, 7, 7, 7, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 28, 34, 34, 34, 22, 23, 11, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 28, 28, 34, 34, 22, 22, 1] 34 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: 137 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: REAL300025241157 none CN(CC1CCCN1C(=O)CS(N)(=O)=O)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 8, 11, 11, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 6, 6, 7, 6, 7, 7, 7, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 13, 13, 13, 4, 6, 6, 10, 13, 23, 23, 23, 23, 23, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 13, 13, 10, 10, 23] 34 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 112 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241157 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241157 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241157/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241157 Building REAL300025241158 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241158' /scratch/stefan/7787021/working/building/REAL300025241158 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241158 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241158/0 /scratch/stefan/7787021/working/building/REAL300025241158 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/9 `/scratch/stefan/7787021/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CC(N)=CC=N1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241158.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241158 none CN(CC1CCCN1C(=O)C1=CC(N)=CC=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 3, 7, 6, 7, 7, 7, 7, 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: [22, 17, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 22, 43, 43, 80, 117, 201, 201, 201, 201, 201, 22, 22, 22, 17, 17, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 80, 80, 201] 201 rigid atoms, others: [43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 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]) total number of confs: 536 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: REAL300025241158 none CN(CC1CCCN1C(=O)C1=CC(N)=CC=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 3, 7, 6, 7, 7, 7, 7, 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: [102, 91, 102, 133, 135, 135, 135, 135, 135, 184, 184, 201, 201, 201, 201, 201, 201, 39, 91, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 102, 133, 133, 135, 135, 135, 135, 135, 135, 135, 201, 201, 201, 201, 201, 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: 735 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: REAL300025241158 none CN(CC1CCCN1C(=O)C1=CC(N)=CC=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 3, 7, 6, 7, 7, 7, 7, 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, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 7, 12, 12, 27, 48, 135, 135, 135, 135, 135, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 27, 27, 135] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 284 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241158 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241158 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241158/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241158 Building REAL300025241159 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241159' /scratch/stefan/7787021/working/building/REAL300025241159 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241159 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241159/0 /scratch/stefan/7787021/working/building/REAL300025241159 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/10 `/scratch/stefan/7787021/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C=C1CCCC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241159.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241159 none CN(CC1CCCN1C(=O)C=C1CCCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7] 0 hydrogens 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, 24, 14, 14, 14, 14, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 36, 65, 65, 101, 125, 201, 201, 201, 201, 201, 36, 36, 36, 24, 24, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 101, 101, 201] 201 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 597 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: REAL300025241159 none CN(CC1CCCN1C(=O)C=C1CCCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7] 0 hydrogens 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, 93, 100, 100, 100, 100, 100, 103, 103, 201, 201, 201, 201, 201, 35, 67, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 93, 93, 100, 100, 100, 100, 100, 100, 100, 201, 201, 201, 201, 201, 201, 201, 201, 201, 35, 35, 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: 728 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: REAL300025241159 none CN(CC1CCCN1C(=O)C=C1CCCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7] 0 hydrogens 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, 1, 4, 4, 14, 14, 14, 14, 14, 9, 17, 17, 34, 46, 100, 100, 100, 100, 100, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 34, 34, 100] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 274 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241159 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241159 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241159/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241159 Building REAL300025241160 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241160' /scratch/stefan/7787021/working/building/REAL300025241160 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241160 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241160/0 /scratch/stefan/7787021/working/building/REAL300025241160 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/11 `/scratch/stefan/7787021/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC(C)(C)C#N)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241160.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241160 none CN(CC1CCCN1C(=O)CC(C)(C)C#N)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 12, 12, 8, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12, 1] 13 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: 37 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: REAL300025241160 none CN(CC1CCCN1C(=O)CC(C)(C)C#N)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 3, 4, 4, 7, 9, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 12] 13 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 53 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241160 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241160 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241160/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241160 Building REAL300025241161 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241161' /scratch/stefan/7787021/working/building/REAL300025241161 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241161 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241161/0 /scratch/stefan/7787021/working/building/REAL300025241161 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/12 `/scratch/stefan/7787021/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC(=O)NC1CC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241161.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241161 none CN(CC1CCCN1C(=O)CC(=O)NC1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 26, 25, 18, 25, 6, 6, 6, 1, 1, 1, 1, 44, 52, 52, 93, 125, 201, 201, 201, 201, 201, 44, 44, 44, 44, 44, 26, 26, 26, 26, 26, 26, 26, 18, 18, 6, 1, 1, 1, 1, 1, 93, 93, 201] 201 rigid atoms, others: [45, 42, 43, 44, 13, 14, 15, 16, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49]) total number of confs: 650 number of broken/clashed sets: 158 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241161 none CN(CC1CCCN1C(=O)CC(=O)NC1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 50, 77, 77, 77, 77, 77, 77, 77, 77, 181, 196, 196, 196, 201, 201, 27, 37, 13, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 77, 77, 77, 77, 77, 77, 77, 77, 77, 181, 181, 196, 201, 201, 201, 201, 201, 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: 880 number of broken/clashed sets: 158 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241161 none CN(CC1CCCN1C(=O)CC(=O)NC1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 3, 3, 6, 8, 8, 8, 26, 26, 4, 5, 5, 10, 15, 77, 77, 77, 77, 77, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 26, 26, 26, 26, 26, 10, 10, 77] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 158 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241161 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241161 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241161/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241161 Building REAL300025241162 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241162' /scratch/stefan/7787021/working/building/REAL300025241162 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241162 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241162/0 /scratch/stefan/7787021/working/building/REAL300025241162 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/13 `/scratch/stefan/7787021/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241162.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241162 none COCC(O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 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] 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, 194, 110, 194, 110, 110, 110, 110, 110, 110, 108, 77, 55, 77, 29, 55, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 194, 582, 110, 110, 110, 110, 110, 110, 110, 108, 108, 77, 77, 77, 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: 1492 number of broken/clashed sets: 417 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241162 none COCC(O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 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] 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, 9, 6, 2, 6, 1, 2, 1, 1, 1, 1, 1, 1, 3, 4, 4, 6, 6, 14, 25, 110, 110, 110, 110, 110, 16, 16, 16, 9, 9, 6, 18, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 14, 14, 110] 603 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 245 number of broken/clashed sets: 417 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241162 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241162 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241162/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241162 Building REAL300025241163 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241163' /scratch/stefan/7787021/working/building/REAL300025241163 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241163 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241163/0 /scratch/stefan/7787021/working/building/REAL300025241163 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/14 `/scratch/stefan/7787021/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C(C)(C)CCCO)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241163.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241163 none CN(CC1CCCN1C(=O)C(C)(C)CCCO)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [160, 107, 160, 185, 199, 199, 199, 199, 199, 199, 199, 199, 199, 199, 201, 201, 201, 32, 107, 13, 1, 1, 1, 1, 1, 1, 1, 160, 160, 160, 185, 185, 199, 199, 199, 199, 199, 199, 199, 199, 199, 199, 199, 199, 199, 201, 201, 201, 201, 201, 201, 603, 32, 32, 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: 1304 number of broken/clashed sets: 603 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241163 none CN(CC1CCCN1C(=O)C(C)(C)CCCO)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 5, 6, 9, 9, 33, 67, 199, 199, 199, 199, 199, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 5, 5, 15, 33, 33, 199] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 395 number of broken/clashed sets: 603 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241163 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241163 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241163/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241163 Building REAL300025241164 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241164' /scratch/stefan/7787021/working/building/REAL300025241164 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241164 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241164/0 /scratch/stefan/7787021/working/building/REAL300025241164 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/15 `/scratch/stefan/7787021/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)C1CCOC1) `REAL300025241164.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241164 none CC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)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', 'C.3', 'N.am', 'C.3', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 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, 196, 201, 196, 196, 196, 196, 193, 157, 105, 157, 31, 105, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 196, 196, 196, 196, 196, 196, 196, 193, 193, 157, 157, 157, 31, 31, 1, 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]) total number of confs: 720 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: REAL300025241164 none CC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)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', 'C.3', 'N.am', 'C.3', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 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: [2, 1, 2, 3, 3, 4, 4, 4, 4, 4, 8, 12, 12, 29, 29, 69, 109, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 8, 8, 12, 12, 12, 69, 69, 201, 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: 491 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: REAL300025241164 none CC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)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', 'C.3', 'N.am', 'C.3', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 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, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 8, 8, 20, 20, 53, 93, 196, 196, 196, 196, 196, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 53, 53, 196, 4, 4, 4, 4, 4, 4, 4] 201 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 37, 31] set([0, 1, 3, 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]) total number of confs: 443 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241164 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241164 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241164/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241164 Building REAL300025241165 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241165' /scratch/stefan/7787021/working/building/REAL300025241165 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241165 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241165/0 /scratch/stefan/7787021/working/building/REAL300025241165 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/16 `/scratch/stefan/7787021/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=COC(Cl)=C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241165.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241165 none CN(CC1CCCN1C(=O)C1=COC(Cl)=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 16, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 6, 7, 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: [28, 20, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 28, 55, 55, 79, 112, 201, 201, 201, 201, 201, 28, 28, 28, 20, 20, 12, 12, 12, 12, 12, 12, 12, 1, 1, 79, 79, 201] 201 rigid atoms, others: [38, 39, 8, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 528 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: REAL300025241165 none CN(CC1CCCN1C(=O)C1=COC(Cl)=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 16, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 6, 7, 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: [65, 64, 65, 88, 97, 97, 97, 97, 97, 140, 140, 201, 201, 201, 201, 201, 34, 64, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 88, 88, 97, 97, 97, 97, 97, 97, 97, 201, 201, 34, 34, 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: 675 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: REAL300025241165 none CN(CC1CCCN1C(=O)C1=COC(Cl)=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 16, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 6, 7, 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, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 7, 13, 13, 20, 32, 97, 97, 97, 97, 97, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 20, 20, 97] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42]) total number of confs: 207 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241165 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241165 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241165/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241165 Building REAL300025241166 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241166' /scratch/stefan/7787021/working/building/REAL300025241166 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241166 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241166/0 /scratch/stefan/7787021/working/building/REAL300025241166 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/17 `/scratch/stefan/7787021/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)[C@H]1C[C@H]([NH+](C)C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241166.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241166 none CN(CC1CCCN1C(=O)[C@H]1C[C@H]([NH+](C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 9, 6, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 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: [14, 11, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 14, 17, 17, 33, 36, 42, 42, 42, 42, 42, 14, 14, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 33, 33, 42] 42 rigid atoms, others: [51, 43, 8, 10, 11, 12, 13, 14, 15, 50, 19, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 52, 53, 54]) total number of confs: 166 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: REAL300025241166 none CN(CC1CCCN1C(=O)[C@H]1C[C@H]([NH+](C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 9, 6, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 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: [36, 34, 36, 36, 36, 36, 36, 36, 36, 37, 37, 42, 42, 42, 42, 42, 42, 42, 42, 42, 19, 34, 12, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 19, 19, 1] 42 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: 139 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: REAL300025241166 none CN(CC1CCCN1C(=O)[C@H]1C[C@H]([NH+](C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 9, 6, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 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: [7, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 10, 10, 10, 7, 7, 9, 9, 21, 25, 36, 36, 36, 36, 36, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 7, 7, 21, 21, 36] 42 rigid atoms, others: [2, 35, 4, 5, 6, 7, 40, 41, 39, 8, 3, 36, 38, 37] 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 138 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241166 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241166 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241166/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241166 Building REAL300025241167 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241167' /scratch/stefan/7787021/working/building/REAL300025241167 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241167 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241167/0 /scratch/stefan/7787021/working/building/REAL300025241167 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/18 `/scratch/stefan/7787021/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC1(C2CC2)CC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241167.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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: REAL300025241167 none CN(CC1CCCN1C(=O)CC1(C2CC2)CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 3, 6, 1, 1, 1, 3, 3, 1, 1, 6, 8, 8, 13, 14, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 13, 13, 15] 15 rigid atoms, others: [48, 10, 11, 12, 46, 15, 16, 49, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52]) total number of confs: 60 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: REAL300025241167 none CN(CC1CCCN1C(=O)CC1(C2CC2)CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 8, 8, 7, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 1] 15 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: 44 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: REAL300025241167 none CN(CC1CCCN1C(=O)CC1(C2CC2)CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 3, 6, 3, 1, 1, 1, 1, 3, 3, 6, 8, 8, 13, 14, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 13, 13, 15] 15 rigid atoms, others: [45, 43, 41, 42, 11, 12, 13, 14, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 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]) total number of confs: 51 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: REAL300025241167 none CN(CC1CCCN1C(=O)CC1(C2CC2)CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 6, 6, 2, 3, 3, 6, 7, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8] 15 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 46 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241167 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241167 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241167/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241167 Building REAL300025241168 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241168' /scratch/stefan/7787021/working/building/REAL300025241168 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241168 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241168/0 /scratch/stefan/7787021/working/building/REAL300025241168 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/19 `/scratch/stefan/7787021/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)[C@@H]1CC1(F)F)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241168.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241168 none CN(CC1CCCN1C(=O)[C@@H]1CC1(F)F)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 10, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 28, 56, 56, 95, 131, 201, 201, 201, 201, 201, 28, 28, 28, 19, 19, 10, 10, 10, 10, 10, 10, 10, 1, 1, 95, 95, 201] 201 rigid atoms, others: [38, 39, 8, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 579 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241168 none CN(CC1CCCN1C(=O)[C@@H]1CC1(F)F)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 105, 112, 149, 155, 155, 155, 155, 155, 160, 160, 201, 201, 201, 201, 201, 41, 105, 13, 1, 1, 1, 1, 1, 1, 1, 112, 112, 112, 149, 149, 155, 155, 155, 155, 155, 155, 155, 201, 201, 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: 751 number of broken/clashed sets: 53 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241168 none CN(CC1CCCN1C(=O)[C@@H]1CC1(F)F)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 1, 5, 5, 10, 10, 10, 10, 10, 9, 19, 19, 42, 68, 155, 155, 155, 155, 155, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 42, 42, 155] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42]) total number of confs: 367 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241168 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241168 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241168/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241168 Building REAL300025241169 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241169' /scratch/stefan/7787021/working/building/REAL300025241169 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241169 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241169/0 /scratch/stefan/7787021/working/building/REAL300025241169 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/20 `/scratch/stefan/7787021/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)[C@@H]1C[C@H]1C#N)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241169.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241169 none CN(CC1CCCN1C(=O)[C@@H]1C[C@H]1C#N)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 10, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 28, 53, 53, 90, 123, 201, 201, 201, 201, 201, 28, 28, 28, 19, 19, 10, 10, 10, 10, 10, 10, 10, 1, 1, 90, 90, 201] 201 rigid atoms, others: [39, 8, 10, 11, 12, 13, 14, 15, 16, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 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]) total number of confs: 565 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: REAL300025241169 none CN(CC1CCCN1C(=O)[C@@H]1C[C@H]1C#N)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 93, 98, 136, 139, 139, 139, 139, 139, 143, 143, 201, 201, 201, 201, 201, 201, 40, 93, 12, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 136, 136, 139, 139, 139, 139, 139, 139, 139, 201, 201, 40, 40, 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: 764 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: REAL300025241169 none CN(CC1CCCN1C(=O)[C@@H]1C[C@H]1C#N)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 10, 10, 10, 19, 19, 39, 56, 139, 139, 139, 139, 139, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 39, 39, 139] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43]) total number of confs: 323 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241169 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241169 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241169/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241169 Building REAL300025241170 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241170' /scratch/stefan/7787021/working/building/REAL300025241170 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241170 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241170/0 /scratch/stefan/7787021/working/building/REAL300025241170 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/21 `/scratch/stefan/7787021/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(CC)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241170.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241170 none CCCC(CC)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 182, 196, 196, 91, 89, 91, 89, 89, 89, 89, 79, 58, 42, 58, 17, 42, 10, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 196, 196, 196, 196, 196, 196, 182, 182, 89, 89, 89, 89, 89, 89, 89, 79, 79, 58, 58, 58, 17, 17, 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: 859 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241170 none CCCC(CC)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 12, 14, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 7, 7, 13, 13, 30, 40, 89, 89, 89, 89, 89, 18, 18, 18, 18, 18, 18, 18, 12, 14, 14, 14, 14, 14, 8, 8, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 30, 30, 89] 201 rigid atoms, others: [45, 43, 7, 9, 42, 11, 12, 13, 46, 44, 48, 14, 47, 10] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 301 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241170 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241170 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241170/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241170 Building REAL300025241171 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241171' /scratch/stefan/7787021/working/building/REAL300025241171 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241171 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241171/0 /scratch/stefan/7787021/working/building/REAL300025241171 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/22 `/scratch/stefan/7787021/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CCCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241171.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241171 none C=C(C)CCCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 115, 53, 53, 53, 53, 53, 53, 53, 53, 37, 31, 37, 22, 31, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 196, 143, 143, 115, 115, 53, 53, 53, 53, 53, 53, 53, 53, 53, 37, 37, 37, 22, 22, 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: 955 number of broken/clashed sets: 149 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241171 none C=C(C)CCCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 17, 26, 9, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 9, 14, 53, 53, 53, 53, 53, 26, 26, 26, 26, 26, 17, 16, 10, 10, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 53] 201 rigid atoms, others: [43, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 209 number of broken/clashed sets: 149 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241171 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241171 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241171/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241171 Building REAL300025241172 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241172' /scratch/stefan/7787021/working/building/REAL300025241172 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241172 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241172/0 /scratch/stefan/7787021/working/building/REAL300025241172 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/23 `/scratch/stefan/7787021/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=NN1C) `REAL300025241172.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241172 none CC1=NC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=NN1C 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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: [8, 8, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 5, 5, 12, 12, 35, 51, 118, 118, 118, 118, 118, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 35, 35, 118, 8, 8, 8] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 36, 30, 31] set([0, 1, 2, 3, 5, 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]) total number of confs: 284 number of broken/clashed sets: 79 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241172 none CC1=NC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=NN1C 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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: [201, 201, 201, 136, 118, 136, 118, 118, 118, 118, 114, 96, 67, 96, 24, 67, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 118, 118, 118, 118, 118, 118, 118, 114, 114, 96, 96, 96, 24, 24, 1, 201, 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]) total number of confs: 603 number of broken/clashed sets: 79 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241172 none CC1=NC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=NN1C 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 1, 6, 6, 8, 8, 8, 8, 8, 15, 18, 18, 36, 36, 87, 114, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 15, 15, 18, 18, 18, 87, 87, 201, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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, 45, 46, 47]) total number of confs: 575 number of broken/clashed sets: 79 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241172 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241172 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241172/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241172 Building REAL300025241173 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241173' /scratch/stefan/7787021/working/building/REAL300025241173 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241173 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241173/0 /scratch/stefan/7787021/working/building/REAL300025241173 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/24 `/scratch/stefan/7787021/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)[C@H]1C[C@@H](O)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241173.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241173 none CN(CC1CCCN1C(=O)[C@H]1C[C@@H](O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 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: [28, 21, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 28, 50, 50, 83, 119, 201, 201, 201, 201, 201, 28, 28, 28, 21, 21, 12, 12, 12, 12, 12, 12, 12, 1, 1, 3, 1, 1, 83, 83, 201] 603 rigid atoms, others: [43, 39, 8, 10, 11, 12, 13, 14, 15, 16, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 44, 45, 46]) total number of confs: 545 number of broken/clashed sets: 171 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241173 none CN(CC1CCCN1C(=O)[C@H]1C[C@@H](O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 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: [89, 86, 89, 119, 123, 123, 123, 123, 123, 125, 125, 201, 201, 201, 201, 201, 201, 38, 86, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 119, 119, 123, 123, 123, 123, 123, 123, 123, 201, 201, 603, 201, 201, 38, 38, 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: 1396 number of broken/clashed sets: 171 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241173 none CN(CC1CCCN1C(=O)[C@H]1C[C@@H](O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 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: [9, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 12, 9, 18, 18, 36, 57, 123, 123, 123, 123, 123, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 36, 12, 12, 36, 36, 123] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 345 number of broken/clashed sets: 171 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241173 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241173 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241173/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241173 Building REAL300025241174 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241174' /scratch/stefan/7787021/working/building/REAL300025241174 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241174 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241174/0 /scratch/stefan/7787021/working/building/REAL300025241174 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/25 `/scratch/stefan/7787021/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC1CC1(C)C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241174.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241174 none CN(CC1CCCN1C(=O)CC1CC1(C)C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 5, 10, 1, 1, 1, 1, 1, 1, 10, 12, 12, 22, 24, 28, 28, 28, 28, 28, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 22, 22, 28] 28 rigid atoms, others: [40, 41, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 107 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: REAL300025241174 none CN(CC1CCCN1C(=O)CC1CC1(C)C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 22, 28, 28, 28, 28, 9, 9, 7, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 22, 22, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 1] 28 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: 98 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: REAL300025241174 none CN(CC1CCCN1C(=O)CC1CC1(C)C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 10, 10, 10, 10, 2, 3, 3, 6, 8, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 9] 28 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 62 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241174 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241174 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241174/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241174 Building REAL300025241175 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241175' /scratch/stefan/7787021/working/building/REAL300025241175 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241175 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241175/0 /scratch/stefan/7787021/working/building/REAL300025241175 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/26 `/scratch/stefan/7787021/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)C(C)(C)C) `REAL300025241175.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241175 none CC(=CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)C(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', 'C.3', 'N.am', 'C.3', 'C.2', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 139, 139, 139, 139, 139, 139, 139, 128, 111, 79, 111, 26, 79, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 139, 139, 139, 139, 139, 139, 139, 128, 128, 111, 111, 111, 26, 26, 1, 201, 201, 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]) total number of confs: 733 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241175 none CC(=CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)C(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', 'C.3', 'N.am', 'C.3', 'C.2', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 6, 6, 15, 15, 37, 56, 139, 139, 139, 139, 139, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 37, 37, 139, 5, 5, 5, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 37, 31] set([0, 1, 2, 4, 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: 315 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241175 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241175 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241175/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241175 Building REAL300025241176 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241176' /scratch/stefan/7787021/working/building/REAL300025241176 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241176 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241176/0 /scratch/stefan/7787021/working/building/REAL300025241176 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/27 `/scratch/stefan/7787021/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=C(Cl)CC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241176.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241176 none CN(CC1CCCN1C(=O)C1=C(Cl)CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 16, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 31, 17, 17, 17, 17, 17, 10, 1, 10, 1, 1, 1, 1, 1, 38, 71, 71, 104, 134, 201, 201, 201, 201, 201, 38, 38, 38, 31, 31, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 104, 104, 201] 201 rigid atoms, others: [37, 38, 39, 8, 10, 11, 12, 13, 14, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43]) total number of confs: 597 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: REAL300025241176 none CN(CC1CCCN1C(=O)C1=C(Cl)CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 16, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 84, 91, 118, 124, 124, 124, 124, 124, 146, 146, 201, 201, 201, 201, 38, 84, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 118, 118, 124, 124, 124, 124, 124, 124, 124, 201, 201, 201, 201, 38, 38, 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: 651 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: REAL300025241176 none CN(CC1CCCN1C(=O)C1=C(Cl)CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 16, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 1, 5, 5, 17, 17, 17, 17, 9, 16, 16, 29, 48, 124, 124, 124, 124, 124, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 29, 29, 124] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 280 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241176 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241176 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241176/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241176 Building REAL300025241177 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241177' /scratch/stefan/7787021/working/building/REAL300025241177 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241177 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241177/0 /scratch/stefan/7787021/working/building/REAL300025241177 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/28 `/scratch/stefan/7787021/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=NN1CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241177.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241177 none CC1=NN=NN1CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 1, 8, 8, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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: [12, 12, 12, 12, 12, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 8, 8, 17, 17, 47, 72, 166, 166, 166, 166, 166, 12, 12, 12, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 47, 47, 166] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 406 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: REAL300025241177 none CC1=NN=NN1CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 1, 8, 8, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 201, 201, 201, 201, 166, 166, 166, 166, 166, 166, 166, 155, 119, 76, 119, 29, 76, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 166, 166, 166, 166, 166, 166, 166, 155, 155, 119, 119, 119, 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: 795 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: REAL300025241177 none CC1=NN=NN1CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 1, 8, 8, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 3, 8, 8, 12, 12, 12, 12, 12, 16, 20, 20, 35, 35, 76, 112, 201, 201, 201, 201, 201, 2, 2, 2, 3, 3, 12, 12, 12, 12, 12, 12, 12, 16, 16, 20, 20, 20, 76, 76, 201] 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: 528 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241177 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241177 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241177/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241177 Building REAL300025241178 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241178' /scratch/stefan/7787021/working/building/REAL300025241178 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241178 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241178/0 /scratch/stefan/7787021/working/building/REAL300025241178 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/29 `/scratch/stefan/7787021/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)[C@]12C[C@H]1[C@H](F)C2)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241178.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241178 none CN(CC1CCCN1C(=O)[C@]12C[C@H]1[C@H](F)C2)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 7, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 12, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 22, 45, 45, 91, 125, 201, 201, 201, 201, 201, 22, 22, 22, 12, 12, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 91, 91, 201] 201 rigid atoms, others: [43, 8, 41, 10, 11, 12, 13, 14, 15, 16, 17, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46]) total number of confs: 544 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241178 none CN(CC1CCCN1C(=O)[C@]12C[C@H]1[C@H](F)C2)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 7, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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: [148, 115, 148, 182, 188, 188, 188, 188, 188, 200, 200, 201, 201, 201, 201, 201, 201, 201, 39, 115, 13, 1, 1, 1, 1, 1, 1, 1, 148, 148, 148, 182, 182, 188, 188, 188, 188, 188, 188, 188, 201, 201, 201, 201, 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: 730 number of broken/clashed sets: 58 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241178 none CN(CC1CCCN1C(=O)[C@]12C[C@H]1[C@H](F)C2)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 7, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 6, 6, 11, 30, 30, 65, 100, 188, 188, 188, 188, 188, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 65, 65, 188] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 39, 34, 35, 36, 38, 37] 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, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 453 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241178 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241178 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241178/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241178 Building REAL300025241179 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241179' /scratch/stefan/7787021/working/building/REAL300025241179 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241179 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241179/0 /scratch/stefan/7787021/working/building/REAL300025241179 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/30 `/scratch/stefan/7787021/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CNC(=O)O1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241179.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241179 none CN(CC1CCCN1C(=O)C1=CNC(=O)O1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 3, 7, 6, 7, 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, 27, 15, 15, 15, 15, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 39, 72, 72, 98, 130, 201, 201, 201, 201, 201, 39, 39, 39, 27, 27, 15, 15, 15, 15, 15, 15, 15, 1, 1, 98, 98, 201] 201 rigid atoms, others: [38, 39, 8, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42]) 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: REAL300025241179 none CN(CC1CCCN1C(=O)C1=CNC(=O)O1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 3, 7, 6, 7, 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: [112, 96, 112, 146, 153, 153, 153, 153, 153, 187, 187, 201, 201, 201, 201, 201, 40, 96, 13, 1, 1, 1, 1, 1, 1, 1, 112, 112, 112, 146, 146, 153, 153, 153, 153, 153, 153, 153, 201, 201, 40, 40, 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: 728 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: REAL300025241179 none CN(CC1CCCN1C(=O)C1=CNC(=O)O1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 3, 7, 6, 7, 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, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 15, 15, 8, 18, 18, 34, 57, 153, 153, 153, 153, 153, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 15, 15, 34, 34, 153] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42]) total number of confs: 333 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241179 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241179 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241179/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241179 Building REAL300025241180 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241180' /scratch/stefan/7787021/working/building/REAL300025241180 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241180 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241180/0 /scratch/stefan/7787021/working/building/REAL300025241180 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/31 `/scratch/stefan/7787021/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1C[C@H]1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241180.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241180 none CC(C)[C@@H]1C[C@H]1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 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: [6, 6, 6, 6, 6, 6, 2, 6, 1, 2, 1, 1, 1, 1, 1, 1, 4, 6, 6, 11, 11, 30, 48, 126, 126, 126, 126, 126, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 30, 30, 126] 201 rigid atoms, others: [43, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 280 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: REAL300025241180 none CC(C)[C@@H]1C[C@H]1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 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: [201, 201, 201, 201, 201, 201, 126, 201, 126, 126, 126, 126, 126, 126, 115, 105, 74, 105, 27, 74, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 126, 126, 126, 126, 126, 126, 126, 115, 115, 105, 105, 105, 27, 27, 1] 201 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: 704 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: REAL300025241180 none CC(C)[C@@H]1C[C@H]1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 12, 15, 15, 29, 29, 68, 105, 201, 201, 201, 201, 201, 2, 2, 2, 2, 2, 2, 2, 1, 1, 6, 6, 6, 6, 6, 6, 6, 12, 12, 15, 15, 15, 68, 68, 201] 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: 524 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241180 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241180 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241180/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241180 Building REAL300025241181 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241181' /scratch/stefan/7787021/working/building/REAL300025241181 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241181 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241181/0 /scratch/stefan/7787021/working/building/REAL300025241181 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/32 `/scratch/stefan/7787021/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CNC(Cl)=N1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241181.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241181 none CN(CC1CCCN1C(=O)C1=CNC(Cl)=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'Cl', 'N.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 16, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 6, 7, 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 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [30, 21, 12, 12, 12, 12, 12, 6, 1, 6, 1, 1, 1, 1, 1, 1, 30, 61, 61, 85, 129, 190, 190, 190, 190, 190, 30, 30, 30, 21, 21, 12, 12, 12, 12, 12, 12, 12, 1, 1, 85, 85, 190] 190 rigid atoms, others: [38, 39, 8, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 524 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: REAL300025241181 none CN(CC1CCCN1C(=O)C1=CNC(Cl)=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'Cl', 'N.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 16, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 6, 7, 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 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [106, 95, 106, 137, 143, 143, 143, 143, 143, 188, 188, 190, 190, 190, 190, 190, 38, 95, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 137, 137, 143, 143, 143, 143, 143, 143, 143, 190, 190, 38, 38, 1] 190 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: 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: REAL300025241181 none CN(CC1CCCN1C(=O)C1=CNC(Cl)=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'Cl', 'N.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 16, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 6, 7, 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 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 12, 12, 12, 12, 9, 18, 18, 27, 47, 143, 143, 143, 143, 143, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 27, 27, 143] 190 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42]) total number of confs: 282 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241181 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241181/1 /scratch/stefan/7787021/working/building/REAL300025241181 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/33 `/scratch/stefan/7787021/working/3D/33' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CN=C(Cl)N1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241181.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241181/1/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: REAL300025241181 none CN(CC1CCCN1C(=O)C1=CN=C(Cl)N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'Cl', 'N.pl3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 16, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 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] 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: [26, 21, 14, 14, 14, 14, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 26, 46, 46, 66, 75, 120, 120, 120, 120, 120, 26, 26, 26, 21, 21, 14, 14, 14, 14, 14, 14, 14, 1, 1, 66, 66, 120] 120 rigid atoms, others: [38, 39, 8, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 354 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: REAL300025241181 none CN(CC1CCCN1C(=O)C1=CN=C(Cl)N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'Cl', 'N.pl3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 16, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 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] 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: [63, 63, 63, 74, 78, 78, 78, 78, 78, 107, 107, 120, 120, 120, 120, 120, 33, 63, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 74, 74, 78, 78, 78, 78, 78, 78, 78, 120, 120, 33, 33, 1] 120 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: 418 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: REAL300025241181 none CN(CC1CCCN1C(=O)C1=CN=C(Cl)N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'Cl', 'N.pl3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 16, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 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] 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: [9, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 14, 14, 14, 9, 14, 14, 25, 33, 78, 78, 78, 78, 78, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 14, 14, 25, 25, 78] 120 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42]) total number of confs: 205 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241181 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241181 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241181/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241181/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241181 Building REAL300025241182 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241182' /scratch/stefan/7787021/working/building/REAL300025241182 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241182 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241182/0 /scratch/stefan/7787021/working/building/REAL300025241182 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/34 `/scratch/stefan/7787021/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CC2CCCC12)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241182.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241182 none CN(CC1CCCN1C(=O)C1=CC2CCCC12)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 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, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 33, 67, 67, 92, 128, 201, 201, 201, 201, 201, 33, 33, 33, 24, 24, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 92, 92, 201] 201 rigid atoms, others: [45, 43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 552 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: REAL300025241182 none CN(CC1CCCN1C(=O)C1=CC2CCCC12)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 82, 88, 116, 120, 120, 120, 120, 120, 157, 157, 201, 201, 201, 201, 201, 201, 37, 82, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 116, 116, 120, 120, 120, 120, 120, 120, 120, 201, 201, 201, 201, 201, 201, 201, 201, 201, 37, 37, 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: 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: REAL300025241182 none CN(CC1CCCN1C(=O)C1=CC2CCCC12)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 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, 7] 0 hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 14, 14, 14, 14, 7, 15, 15, 26, 41, 120, 120, 120, 120, 120, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 26, 26, 120] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 255 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241182 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241182 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241182/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241182 Building REAL300025241183 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241183' /scratch/stefan/7787021/working/building/REAL300025241183 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241183 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241183/0 /scratch/stefan/7787021/working/building/REAL300025241183 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/35 `/scratch/stefan/7787021/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=CN=C1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241183.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241183 none CCN1N=CN=C1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 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: [10, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 7, 7, 14, 14, 34, 57, 156, 156, 156, 156, 156, 10, 10, 10, 10, 10, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 34, 34, 156] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 348 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241183 none CCN1N=CN=C1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 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: [201, 184, 184, 184, 184, 184, 160, 156, 160, 156, 156, 156, 156, 152, 111, 79, 111, 26, 78, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 184, 156, 156, 156, 156, 156, 156, 156, 152, 152, 111, 111, 111, 26, 26, 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: 759 number of broken/clashed sets: 77 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241183 none CCN1N=CN=C1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 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: [4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 10, 14, 14, 23, 23, 52, 77, 184, 184, 184, 184, 184, 4, 4, 4, 4, 4, 1, 5, 5, 5, 5, 5, 5, 5, 10, 10, 14, 14, 14, 52, 52, 184] 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: 427 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241183 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241183 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241183/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241183 Building REAL300025241184 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241184' /scratch/stefan/7787021/working/building/REAL300025241184 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241184 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241184/0 /scratch/stefan/7787021/working/building/REAL300025241184 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/36 `/scratch/stefan/7787021/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)COCCO)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241184.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241184 none CN(CC1CCCN1C(=O)COCCO)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 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] 1 hydrogens need rotated 417 conformations in input total number of sets (complete confs): 417 using faster count positions algorithm for large data unique positions, atoms: [20, 14, 20, 22, 27, 27, 27, 27, 27, 27, 27, 95, 135, 139, 139, 9, 14, 7, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 22, 22, 27, 27, 27, 27, 27, 27, 27, 95, 95, 139, 139, 139, 139, 417, 9, 9, 1] 417 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: 864 number of broken/clashed sets: 117 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241184 none CN(CC1CCCN1C(=O)COCCO)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 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] 1 hydrogens need rotated 417 conformations in input total number of sets (complete confs): 417 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 40, 59, 64, 6, 9, 9, 11, 14, 27, 27, 27, 27, 27, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 59, 59, 64, 64, 192, 11, 11, 27] 417 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 477 number of broken/clashed sets: 117 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241184 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241184 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241184/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241184 Building REAL300025241185 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241185' /scratch/stefan/7787021/working/building/REAL300025241185 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241185 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241185/0 /scratch/stefan/7787021/working/building/REAL300025241185 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/37 `/scratch/stefan/7787021/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=NOC(C)(C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241185.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241185 none CN(CC1CCCN1C(=O)C1=NOC(C)(C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 12, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 37, 69, 69, 100, 132, 201, 201, 201, 201, 201, 37, 37, 37, 30, 30, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 1, 1, 100, 100, 201] 201 rigid atoms, others: [45, 8, 10, 11, 12, 13, 14, 15, 16, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 604 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: REAL300025241185 none CN(CC1CCCN1C(=O)C1=NOC(C)(C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 12, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 78, 87, 115, 121, 121, 121, 121, 121, 156, 156, 201, 201, 201, 201, 201, 201, 36, 78, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 115, 115, 121, 121, 121, 121, 121, 121, 121, 201, 201, 201, 201, 201, 201, 201, 201, 36, 36, 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: 670 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: REAL300025241185 none CN(CC1CCCN1C(=O)C1=NOC(C)(C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 12, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 16, 16, 16, 16, 9, 16, 16, 27, 42, 121, 121, 121, 121, 121, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 27, 27, 121] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 262 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241185 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241185 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241185/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241185 Building REAL300025241186 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241186' /scratch/stefan/7787021/working/building/REAL300025241186 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241186 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241186/0 /scratch/stefan/7787021/working/building/REAL300025241186 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/38 `/scratch/stefan/7787021/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=NC=C(F)C=N1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241186.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241186 none CN(CC1CCCN1C(=O)C1=NC=C(F)C=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 15, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 6, 7, 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, 23, 14, 14, 14, 14, 14, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 32, 51, 51, 78, 117, 201, 201, 201, 201, 201, 32, 32, 32, 23, 23, 14, 14, 14, 14, 14, 14, 14, 1, 1, 78, 78, 201] 201 rigid atoms, others: [39, 8, 10, 11, 12, 13, 14, 15, 16, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 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]) total number of confs: 533 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: REAL300025241186 none CN(CC1CCCN1C(=O)C1=NC=C(F)C=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 15, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 6, 7, 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: [106, 93, 106, 140, 146, 146, 146, 146, 146, 179, 179, 201, 201, 179, 179, 201, 201, 36, 93, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 140, 140, 146, 146, 146, 146, 146, 146, 146, 201, 201, 36, 36, 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: 798 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: REAL300025241186 none CN(CC1CCCN1C(=O)C1=NC=C(F)C=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 15, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 6, 7, 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, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 5, 5, 10, 10, 8, 18, 18, 43, 68, 146, 146, 146, 146, 146, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 43, 43, 146] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43]) total number of confs: 365 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241186 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241186 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241186/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241186 Building REAL300025241187 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241187' /scratch/stefan/7787021/working/building/REAL300025241187 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241187 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241187/0 /scratch/stefan/7787021/working/building/REAL300025241187 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/39 `/scratch/stefan/7787021/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241187.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241187 none CC(C)[C@@H](O)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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, 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, 188, 201, 187, 188, 188, 145, 145, 145, 145, 145, 145, 145, 141, 124, 77, 124, 27, 77, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 564, 187, 187, 145, 145, 145, 145, 145, 145, 145, 141, 141, 124, 124, 124, 27, 27, 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: 1355 number of broken/clashed sets: 348 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241187 none CC(C)[C@@H](O)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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, 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, 10, 15, 7, 10, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 5, 5, 10, 10, 29, 52, 145, 145, 145, 145, 145, 15, 15, 15, 15, 15, 15, 15, 30, 7, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 29, 29, 145] 603 rigid atoms, others: [43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 376 number of broken/clashed sets: 348 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241187 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241187 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241187/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241187 Building REAL300025241188 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241188' /scratch/stefan/7787021/working/building/REAL300025241188 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241188 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241188/0 /scratch/stefan/7787021/working/building/REAL300025241188 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/40 `/scratch/stefan/7787021/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241188.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241188 none C=CCC(C)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 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: [201, 201, 162, 111, 162, 111, 111, 111, 111, 111, 111, 108, 85, 61, 85, 27, 61, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 162, 162, 162, 162, 111, 111, 111, 111, 111, 111, 111, 108, 108, 85, 85, 85, 27, 27, 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: 939 number of broken/clashed sets: 144 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241188 none C=CCC(C)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 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: [14, 9, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 3, 4, 4, 6, 6, 15, 27, 111, 111, 111, 111, 111, 14, 14, 14, 9, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 15, 15, 111] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 242 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241188 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241188 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241188/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241188 Building REAL300025241189 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241189' /scratch/stefan/7787021/working/building/REAL300025241189 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241189 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241189/0 /scratch/stefan/7787021/working/building/REAL300025241189 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/41 `/scratch/stefan/7787021/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)S1) `REAL300025241189.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241189 none CC1CCC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 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, 7, 7, 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, 7] 0 hydrogens 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, 4, 7, 7, 22, 22, 57, 89, 182, 182, 182, 182, 182, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 57, 57, 182] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 431 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241189 none CC1CCC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 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, 7, 7, 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, 7] 0 hydrogens need 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, 183, 182, 183, 182, 182, 182, 182, 173, 146, 91, 146, 30, 91, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 182, 182, 182, 182, 182, 182, 182, 173, 173, 146, 146, 146, 30, 30, 1] 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]) total number of confs: 719 number of broken/clashed sets: 92 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241189 none CC1CCC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 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, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations 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, 4, 4, 6, 6, 6, 6, 6, 11, 15, 15, 37, 37, 77, 112, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 11, 11, 15, 15, 15, 77, 77, 201] 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: 510 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241189 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241189 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241189/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241189 Building REAL300025241190 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241190' /scratch/stefan/7787021/working/building/REAL300025241190 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241190 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241190/0 /scratch/stefan/7787021/working/building/REAL300025241190 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/42 `/scratch/stefan/7787021/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCC1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241190.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241190 none CC1CCCC1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 9, 9, 18, 18, 42, 68, 143, 143, 143, 143, 143, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 42, 42, 143] 201 rigid atoms, others: [43, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 327 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241190 none CC1CCCC1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 151, 143, 151, 143, 143, 143, 143, 138, 113, 96, 113, 37, 96, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 143, 143, 143, 143, 143, 143, 143, 138, 138, 113, 113, 113, 37, 37, 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: 768 number of broken/clashed sets: 63 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241190 none CC1CCCC1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 201 conformations 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, 6, 6, 6, 6, 6, 12, 20, 20, 42, 42, 82, 119, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 12, 12, 20, 20, 20, 82, 82, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 35, 36, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 526 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241190 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241190 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241190/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241190 Building REAL300025241191 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241191' /scratch/stefan/7787021/working/building/REAL300025241191 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241191 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241191/0 /scratch/stefan/7787021/working/building/REAL300025241191 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/43 `/scratch/stefan/7787021/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1C2C3CC1CC32)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241191.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241191 none CN(CC1CCCN1C(=O)C1C2C3CC1CC32)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 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, 7] 0 hydrogens 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, 9, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 20, 41, 41, 85, 126, 201, 201, 201, 201, 201, 20, 20, 20, 9, 9, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 85, 85, 201] 201 rigid atoms, others: [45, 43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 523 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: REAL300025241191 none CN(CC1CCCN1C(=O)C1C2C3CC1CC32)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 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, 7] 0 hydrogens 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, 116, 149, 186, 192, 192, 192, 192, 192, 201, 201, 201, 201, 201, 201, 201, 201, 41, 116, 13, 1, 1, 1, 1, 1, 1, 1, 149, 149, 149, 186, 186, 192, 192, 192, 192, 192, 192, 192, 201, 201, 201, 201, 201, 201, 201, 201, 201, 41, 41, 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: 748 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: REAL300025241191 none CN(CC1CCCN1C(=O)C1C2C3CC1CC32)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 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, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 11, 27, 27, 64, 101, 192, 192, 192, 192, 192, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 64, 64, 192] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 457 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241191 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241191 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241191/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241191 Building REAL300025241192 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241192' /scratch/stefan/7787021/working/building/REAL300025241192 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241192 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241192/0 /scratch/stefan/7787021/working/building/REAL300025241192 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/44 `/scratch/stefan/7787021/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)[C@@H](O)C1CCCC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241192.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241192 none CN(CC1CCCN1C(=O)[C@@H](O)C1CCCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 5, 6, 1, 5, 5, 1, 1, 1, 1, 1, 6, 7, 7, 12, 14, 18, 18, 18, 18, 18, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 18] 54 rigid atoms, others: [48, 45, 49, 41, 10, 43, 44, 13, 14, 15, 16, 17, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 74 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: REAL300025241192 none CN(CC1CCCN1C(=O)[C@@H](O)C1CCCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 18, 18, 18, 18, 18, 18, 18, 14, 14, 10, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 54, 18, 18, 18, 18, 18, 18, 18, 18, 18, 14, 14, 1] 54 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: 107 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: REAL300025241192 none CN(CC1CCCN1C(=O)[C@@H](O)C1CCCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 6, 6, 6, 6, 3, 4, 4, 7, 9, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 15, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 14] 54 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 39, 34, 35, 36, 38, 37] 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 72 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241192 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241192 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241192/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241192 Building REAL300025241193 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241193' /scratch/stefan/7787021/working/building/REAL300025241193 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241193 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241193/0 /scratch/stefan/7787021/working/building/REAL300025241193 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/45 `/scratch/stefan/7787021/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(C)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241193.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241193 none CNC(=O)NC(C)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 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, 4, 7, 6, 4, 7, 7, 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: [201, 201, 201, 201, 198, 178, 198, 178, 178, 178, 178, 178, 178, 165, 128, 78, 128, 27, 78, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 198, 198, 198, 198, 178, 178, 178, 178, 178, 178, 178, 165, 165, 128, 128, 128, 27, 27, 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: 790 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: REAL300025241193 none CNC(=O)NC(C)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 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, 4, 7, 6, 4, 7, 7, 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: [10, 9, 9, 9, 6, 3, 6, 1, 3, 1, 1, 1, 1, 1, 1, 4, 8, 8, 17, 17, 40, 66, 178, 178, 178, 178, 178, 10, 10, 10, 10, 9, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 40, 40, 178] 201 rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 388 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241193 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241193 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241193/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241193 Building REAL300025241194 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241194' /scratch/stefan/7787021/working/building/REAL300025241194 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241194 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241194/0 /scratch/stefan/7787021/working/building/REAL300025241194 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/46 `/scratch/stefan/7787021/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=NN=C1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241194.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241194 none CCN1C=NN=C1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 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: [9, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 10, 10, 18, 18, 38, 62, 165, 165, 165, 165, 165, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 38, 38, 165] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 366 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241194 none CCN1C=NN=C1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 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: [201, 184, 184, 184, 184, 184, 166, 165, 166, 165, 165, 165, 165, 159, 117, 76, 117, 29, 76, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 184, 165, 165, 165, 165, 165, 165, 165, 159, 159, 117, 117, 117, 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: 779 number of broken/clashed sets: 61 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241194 none CCN1C=NN=C1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 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: [4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 9, 17, 17, 27, 27, 52, 78, 184, 184, 184, 184, 184, 4, 4, 4, 4, 4, 1, 5, 5, 5, 5, 5, 5, 5, 9, 9, 17, 17, 17, 52, 52, 184] 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: 434 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241194 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241194 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241194/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241194 Building REAL300025241195 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241195' /scratch/stefan/7787021/working/building/REAL300025241195 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241195 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241195/0 /scratch/stefan/7787021/working/building/REAL300025241195 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/47 `/scratch/stefan/7787021/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1(C2CCC2)CC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241195.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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: REAL300025241195 none CN(CC1CCCN1C(=O)C1(C2CCC2)CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 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: [4, 3, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 3, 3, 3, 1, 1, 4, 5, 5, 5, 6, 8, 8, 8, 8, 8, 4, 4, 4, 3, 3, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 8] 9 rigid atoms, others: [48, 8, 10, 11, 46, 15, 16, 49, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52]) 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.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: REAL300025241195 none CN(CC1CCCN1C(=O)C1(C2CCC2)CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 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, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 1] 9 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: 23 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: REAL300025241195 none CN(CC1CCCN1C(=O)C1(C2CCC2)CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 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, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 5, 6, 6, 6, 7, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 6, 9] 9 rigid atoms, others: [45, 43, 39, 40, 41, 10, 11, 12, 13, 14, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 29 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: REAL300025241195 none CN(CC1CCCN1C(=O)C1(C2CCC2)CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 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: [4, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 2, 2, 4, 5, 5, 5, 6, 8, 8, 8, 8, 8, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 5, 5, 8] 9 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241195 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241195 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241195/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241195 Building REAL300025241196 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241196' /scratch/stefan/7787021/working/building/REAL300025241196 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241196 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241196/0 /scratch/stefan/7787021/working/building/REAL300025241196 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/48 `/scratch/stefan/7787021/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)[C@@H]1CC[C@@H]2C[C@@H]21)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241196.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241196 none CN(CC1CCCN1C(=O)[C@@H]1CC[C@@H]2C[C@@H]21)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 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: [18, 8, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 39, 39, 84, 120, 201, 201, 201, 201, 201, 18, 18, 18, 8, 8, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 84, 84, 201] 201 rigid atoms, others: [45, 43, 8, 41, 10, 11, 12, 13, 14, 44, 16, 17, 18, 46, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 512 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241196 none CN(CC1CCCN1C(=O)[C@@H]1CC[C@@H]2C[C@@H]21)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 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: [164, 124, 164, 195, 199, 199, 199, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 42, 124, 12, 1, 1, 1, 1, 1, 1, 1, 164, 164, 164, 195, 195, 199, 199, 199, 199, 199, 199, 199, 201, 201, 201, 201, 201, 201, 42, 42, 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: 719 number of broken/clashed sets: 61 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241196 none CN(CC1CCCN1C(=O)[C@@H]1CC[C@@H]2C[C@@H]21)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 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: [11, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 11, 29, 29, 72, 109, 199, 199, 199, 199, 199, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 72, 72, 199] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 40, 39, 34, 8, 35, 36, 38, 37] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 487 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241196 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241196 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241196/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241196 Building REAL300025241197 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241197' /scratch/stefan/7787021/working/building/REAL300025241197 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241197 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241197/0 /scratch/stefan/7787021/working/building/REAL300025241197 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/49 `/scratch/stefan/7787021/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)N1) `REAL300025241197.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241197 none CCC1=CC=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)N1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 16, 26, 70, 70, 70, 70, 70, 7, 12, 12, 12, 12, 12, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 70, 7] 201 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 186 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241197 none CCC1=CC=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)N1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 129, 129, 96, 70, 96, 70, 70, 70, 70, 70, 55, 40, 55, 24, 40, 13, 1, 1, 1, 1, 1, 1, 1, 129, 201, 201, 201, 201, 201, 129, 129, 70, 70, 70, 70, 70, 70, 70, 70, 70, 55, 55, 55, 24, 24, 1, 129] 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, 49]) total number of confs: 860 number of broken/clashed sets: 120 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241197 none CCC1=CC=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)N1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 12, 12, 12, 16, 16, 36, 54, 129, 129, 129, 129, 129, 1, 3, 3, 3, 3, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 36, 36, 129, 1] 201 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: 317 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241197 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241197 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241197/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241197 Building REAL300025241198 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241198' /scratch/stefan/7787021/working/building/REAL300025241198 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241198 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241198/0 /scratch/stefan/7787021/working/building/REAL300025241198 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/50 `/scratch/stefan/7787021/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C#CC1CCCO1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241198.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241198 none CN(CC1CCCN1C(=O)C#CC1CCCO1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 31, 31, 67, 105, 201, 201, 201, 201, 201, 15, 15, 15, 9, 9, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 67, 67, 201] 201 rigid atoms, others: [45, 43, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 481 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: REAL300025241198 none CN(CC1CCCN1C(=O)C#CC1CCCO1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 93, 136, 163, 183, 183, 183, 183, 183, 201, 201, 201, 201, 201, 201, 201, 201, 25, 93, 13, 1, 1, 1, 1, 1, 1, 1, 136, 136, 136, 163, 163, 183, 183, 183, 183, 183, 183, 183, 201, 201, 201, 201, 201, 201, 201, 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: 701 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: REAL300025241198 none CN(CC1CCCN1C(=O)C#CC1CCCO1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 21, 21, 54, 91, 183, 183, 183, 183, 183, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 54, 54, 183] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 428 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241198 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241198 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241198/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241198 Building REAL300025241199 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241199' /scratch/stefan/7787021/working/building/REAL300025241199 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241199 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241199/0 /scratch/stefan/7787021/working/building/REAL300025241199 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/51 `/scratch/stefan/7787021/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241199.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241199 none C[C@@H]1C[C@H]1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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: [12, 12, 12, 12, 5, 12, 1, 5, 1, 1, 1, 1, 1, 1, 3, 9, 9, 15, 15, 30, 51, 116, 116, 116, 116, 116, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 30, 30, 116] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 282 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: REAL300025241199 none C[C@@H]1C[C@H]1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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: [201, 201, 201, 201, 122, 201, 116, 122, 116, 116, 116, 116, 113, 89, 85, 89, 36, 85, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 116, 116, 116, 116, 116, 116, 116, 113, 113, 89, 89, 89, 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: 778 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: REAL300025241199 none C[C@@H]1C[C@H]1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 7, 7, 12, 12, 12, 12, 12, 20, 28, 28, 47, 47, 78, 120, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 12, 12, 12, 12, 12, 12, 12, 20, 20, 28, 28, 28, 78, 78, 201] 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: 545 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241199 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241199 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241199/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241199 Building REAL300025241200 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241200' /scratch/stefan/7787021/working/building/REAL300025241200 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241200 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241200/0 /scratch/stefan/7787021/working/building/REAL300025241200 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/52 `/scratch/stefan/7787021/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C[NH+]1CCCCC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241200.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241200 none CN(CC1CCCN1C(=O)C[NH+]1CCCCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [20, 18, 17, 17, 17, 17, 17, 8, 3, 8, 1, 1, 1, 1, 1, 1, 1, 1, 20, 29, 29, 62, 98, 170, 170, 170, 170, 170, 20, 20, 20, 18, 18, 17, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 62, 170] 170 rigid atoms, others: [48, 45, 43, 49, 44, 10, 11, 12, 13, 14, 15, 16, 17, 50, 51, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53, 54]) total number of confs: 424 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241200 none CN(CC1CCCN1C(=O)C[NH+]1CCCCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [124, 101, 124, 147, 147, 147, 147, 147, 147, 156, 156, 169, 170, 170, 170, 170, 170, 170, 35, 101, 13, 1, 1, 1, 1, 1, 1, 1, 124, 124, 124, 147, 147, 147, 147, 147, 147, 147, 147, 147, 169, 169, 170, 170, 170, 170, 170, 170, 170, 170, 170, 170, 35, 35, 1] 170 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: 627 number of broken/clashed sets: 63 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241200 none CN(CC1CCCN1C(=O)C[NH+]1CCCCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 17, 17, 17, 17, 17, 17, 5, 10, 10, 30, 56, 147, 147, 147, 147, 147, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 30, 30, 147] 170 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 39, 34, 35, 36, 38, 37] 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 349 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241200 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241200/1 /scratch/stefan/7787021/working/building/REAL300025241200 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/53 `/scratch/stefan/7787021/working/3D/53' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CN1CCCCC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241200.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241200/1/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: REAL300025241200 none CN(CC1CCCN1C(=O)CN1CCCCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 6, 6, 6, 6, 6, 4, 6, 1, 1, 1, 1, 1, 1, 1, 16, 34, 34, 77, 111, 201, 201, 201, 201, 201, 16, 16, 16, 12, 12, 6, 6, 6, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 77, 77, 201] 201 rigid atoms, others: [48, 45, 43, 47, 41, 10, 11, 12, 13, 14, 44, 16, 49, 50, 46, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53]) total number of confs: 524 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241200 none CN(CC1CCCN1C(=O)CN1CCCCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 83, 121, 146, 158, 158, 158, 158, 158, 158, 158, 201, 201, 201, 201, 201, 201, 28, 83, 13, 1, 1, 1, 1, 1, 1, 1, 121, 121, 121, 146, 146, 158, 158, 158, 158, 158, 158, 158, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 28, 28, 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: 827 number of broken/clashed sets: 78 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241200 none CN(CC1CCCN1C(=O)CN1CCCCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 6, 6, 6, 6, 6, 6, 15, 15, 40, 65, 158, 158, 158, 158, 158, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 40, 40, 158] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 354 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241200 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241200 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241200/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241200/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241200 Building REAL300025241201 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241201' /scratch/stefan/7787021/working/building/REAL300025241201 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241201 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241201/0 /scratch/stefan/7787021/working/building/REAL300025241201 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/54 `/scratch/stefan/7787021/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1CCC[N@H+](C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241201.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241201 none CN(CC1CCCN1C(=O)C1CCC[N@H+](C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 22, 27, 38, 38, 38, 38, 38, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 22, 22, 38] 38 rigid atoms, others: [45, 43, 8, 41, 10, 11, 12, 13, 14, 44, 16, 17, 50, 51, 46, 40, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 52, 53, 54]) total number of confs: 117 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: REAL300025241201 none CN(CC1CCCN1C(=O)C1CCC[N@H+](C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [37, 36, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 22, 36, 12, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 22, 22, 1] 38 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: 123 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: REAL300025241201 none CN(CC1CCCN1C(=O)C1CCC[N@H+](C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 17, 26, 38, 38, 38, 38, 38, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 38] 38 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 39, 34, 35, 36, 38, 37] 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 109 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241201 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241201/1 /scratch/stefan/7787021/working/building/REAL300025241201 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/55 `/scratch/stefan/7787021/working/3D/55' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1CCC[N@@H+](C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241201.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241201/1/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: REAL300025241201 none CN(CC1CCCN1C(=O)C1CCC[N@@H+](C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 10, 12, 12, 17, 19, 22, 22, 22, 22, 22, 10, 10, 10, 8, 8, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 17, 17, 22] 22 rigid atoms, others: [45, 43, 8, 41, 10, 11, 12, 13, 14, 44, 16, 17, 50, 51, 46, 40, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 52, 53, 54]) total number of confs: 78 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: REAL300025241201 none CN(CC1CCCN1C(=O)C1CCC[N@@H+](C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 18, 18, 20, 20, 20, 20, 20, 20, 22, 22, 22, 22, 22, 22, 22, 22, 22, 16, 18, 11, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 20, 20, 20, 20, 20, 20, 20, 20, 20, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 16, 16, 1] 22 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: 67 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: REAL300025241201 none CN(CC1CCCN1C(=O)C1CCC[N@@H+](C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 13, 15, 20, 20, 20, 20, 20, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 20] 22 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 39, 34, 35, 36, 38, 37] 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 75 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241201 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241201 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241201/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241201/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241201 Building REAL300025241202 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241202' /scratch/stefan/7787021/working/building/REAL300025241202 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241202 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241202/0 /scratch/stefan/7787021/working/building/REAL300025241202 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/56 `/scratch/stefan/7787021/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C[N+]1=CN(C)C=C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241202.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241202 none CN(CC1CCCN1C(=O)C[N+]1=CN(C)C=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 5, 1, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 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 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 6, 4, 7, 1, 1, 1, 1, 1, 1, 1, 11, 12, 12, 28, 33, 61, 61, 61, 61, 61, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 1, 2, 2, 2, 1, 1, 28, 28, 61] 61 rigid atoms, others: [45, 41, 10, 11, 12, 13, 14, 15, 16, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 47, 48, 49]) total number of confs: 174 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: REAL300025241202 none CN(CC1CCCN1C(=O)C[N+]1=CN(C)C=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 5, 1, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 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 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [54, 47, 54, 54, 54, 54, 54, 54, 54, 54, 54, 57, 61, 61, 61, 61, 61, 31, 47, 12, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 57, 57, 61, 61, 61, 61, 61, 61, 31, 31, 1] 61 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: 206 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: REAL300025241202 none CN(CC1CCCN1C(=O)C[N+]1=CN(C)C=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 5, 1, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 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 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 3, 4, 4, 14, 20, 54, 54, 54, 54, 54, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 11, 14, 14, 54] 61 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 137 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241202 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241202 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241202/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241202 Building REAL300025241203 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241203' /scratch/stefan/7787021/working/building/REAL300025241203 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241203 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241203/0 /scratch/stefan/7787021/working/building/REAL300025241203 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/57 `/scratch/stefan/7787021/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=CN=C1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241203.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241203 none CC1=NC=CN=C1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 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: [6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 7, 7, 14, 14, 38, 64, 149, 149, 149, 149, 149, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 38, 38, 149] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 332 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241203 none CC1=NC=CN=C1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 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: [201, 201, 201, 201, 201, 201, 153, 149, 153, 149, 149, 149, 149, 144, 118, 79, 118, 28, 78, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 149, 149, 149, 149, 149, 149, 149, 144, 144, 118, 118, 118, 28, 28, 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: 648 number of broken/clashed sets: 81 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241203 none CC1=NC=CN=C1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 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, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 10, 15, 15, 32, 32, 84, 120, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 6, 6, 6, 6, 6, 6, 6, 10, 10, 15, 15, 15, 84, 84, 201] 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: 546 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241203 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241203 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241203/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241203 Building REAL300025241204 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241204' /scratch/stefan/7787021/working/building/REAL300025241204 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241204 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241204/0 /scratch/stefan/7787021/working/building/REAL300025241204 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/58 `/scratch/stefan/7787021/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=NOCC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241204.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241204 none CN(CC1CCCN1C(=O)C1=NOCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 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, 27, 17, 17, 17, 17, 17, 8, 1, 8, 1, 1, 1, 1, 1, 39, 63, 63, 89, 120, 201, 201, 201, 201, 201, 39, 39, 39, 27, 27, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 89, 89, 201] 201 rigid atoms, others: [37, 38, 39, 8, 10, 11, 12, 13, 14, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43]) total number of confs: 536 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: REAL300025241204 none CN(CC1CCCN1C(=O)C1=NOCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 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: [98, 88, 98, 128, 138, 138, 138, 138, 138, 165, 165, 201, 201, 201, 201, 39, 88, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 128, 128, 138, 138, 138, 138, 138, 138, 138, 201, 201, 201, 201, 39, 39, 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: 705 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: REAL300025241204 none CN(CC1CCCN1C(=O)C1=NOCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 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, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 17, 17, 10, 18, 18, 30, 48, 138, 138, 138, 138, 138, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 30, 30, 138] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 300 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241204 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241204 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241204/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241204 Building REAL300025241205 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241205' /scratch/stefan/7787021/working/building/REAL300025241205 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241205 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241205/0 /scratch/stefan/7787021/working/building/REAL300025241205 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/59 `/scratch/stefan/7787021/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)COC1=NOC=C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241205.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241205 none CN(CC1CCCN1C(=O)COC1=NOC=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 8, 12, 1, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 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: [31, 31, 20, 20, 20, 20, 20, 20, 9, 19, 4, 1, 1, 1, 1, 1, 1, 31, 35, 35, 68, 98, 201, 201, 201, 201, 201, 31, 31, 31, 31, 31, 20, 20, 20, 20, 20, 20, 20, 9, 9, 1, 1, 68, 68, 201] 201 rigid atoms, others: [41, 42, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 539 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: REAL300025241205 none CN(CC1CCCN1C(=O)COC1=NOC=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 8, 12, 1, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 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: [55, 43, 55, 76, 76, 76, 76, 76, 76, 76, 76, 170, 201, 201, 201, 201, 201, 26, 43, 13, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 76, 76, 76, 76, 76, 76, 76, 76, 76, 170, 170, 201, 201, 26, 26, 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: 796 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: REAL300025241205 none CN(CC1CCCN1C(=O)COC1=NOC=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 8, 12, 1, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 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: [3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 17, 20, 20, 20, 20, 3, 4, 4, 10, 17, 76, 76, 76, 76, 76, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 10, 10, 76] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 169 number of broken/clashed sets: 156 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241205 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241205 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241205/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241205 Building REAL300025241206 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241206' /scratch/stefan/7787021/working/building/REAL300025241206 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241206 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241206/0 /scratch/stefan/7787021/working/building/REAL300025241206 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/60 `/scratch/stefan/7787021/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=C1C) `REAL300025241206.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241206 none CC1=COC(C(=O)N2CCCC2CN(C)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', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 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: [7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 7, 7, 15, 15, 41, 66, 156, 156, 156, 156, 156, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 41, 41, 156, 7, 7, 7] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 349 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: REAL300025241206 none CC1=COC(C(=O)N2CCCC2CN(C)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', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 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: [201, 201, 201, 201, 163, 156, 163, 156, 156, 156, 156, 150, 120, 79, 120, 29, 79, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 156, 156, 156, 156, 156, 156, 156, 150, 150, 120, 120, 120, 29, 29, 1, 201, 201, 201] 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]) total number of confs: 680 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: REAL300025241206 none CC1=COC(C(=O)N2CCCC2CN(C)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', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 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, 1, 1, 5, 5, 7, 7, 7, 7, 7, 13, 19, 19, 36, 36, 82, 117, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 7, 7, 7, 7, 7, 7, 7, 13, 13, 19, 19, 19, 82, 82, 201, 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: 556 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241206 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241206 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241206/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241206 Building REAL300025241207 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241207' /scratch/stefan/7787021/working/building/REAL300025241207 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241207 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241207/0 /scratch/stefan/7787021/working/building/REAL300025241207 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/61 `/scratch/stefan/7787021/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC1=CN=CC=N1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241207.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241207 none CN(CC1CCCN1C(=O)CC1=CN=CC=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 6, 7, 7, 7, 7, 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: [17, 15, 8, 8, 8, 8, 8, 7, 4, 7, 1, 1, 1, 1, 1, 1, 1, 17, 39, 39, 82, 114, 201, 201, 201, 201, 201, 17, 17, 17, 15, 15, 8, 8, 8, 8, 8, 8, 8, 4, 4, 1, 1, 1, 82, 82, 201] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 15, 16, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46]) total number of confs: 554 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241207 none CN(CC1CCCN1C(=O)CC1=CN=CC=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 6, 7, 7, 7, 7, 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: [102, 69, 102, 120, 126, 126, 126, 126, 126, 127, 127, 201, 201, 201, 201, 201, 201, 26, 69, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 102, 120, 120, 126, 126, 126, 126, 126, 126, 126, 201, 201, 201, 201, 201, 26, 26, 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: 864 number of broken/clashed sets: 71 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241207 none CN(CC1CCCN1C(=O)CC1=CN=CC=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 6, 7, 7, 7, 7, 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: [5, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 8, 8, 8, 8, 8, 5, 12, 12, 32, 47, 126, 126, 126, 126, 126, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 8, 8, 8, 32, 32, 126] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 290 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241207 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241207 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241207/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241207 Building REAL300025241208 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241208' /scratch/stefan/7787021/working/building/REAL300025241208 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241208 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241208/0 /scratch/stefan/7787021/working/building/REAL300025241208 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/62 `/scratch/stefan/7787021/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C#N)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241208.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241208 none CC(C#N)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 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 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 27, 30, 30, 17, 16, 17, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 27, 27, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1] 30 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: 119 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: REAL300025241208 none CC(C#N)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 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 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 7, 9, 16, 16, 16, 16, 16, 10, 10, 10, 10, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 16] 30 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 80 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241208 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241208 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241208/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241208 Building REAL300025241209 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241209' /scratch/stefan/7787021/working/building/REAL300025241209 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241209 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241209/0 /scratch/stefan/7787021/working/building/REAL300025241209 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/63 `/scratch/stefan/7787021/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CC(N)=CC=N1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241209.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241209 none CN(CC1CCCN1C(=O)C1=CC(N)=CC=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 3, 7, 6, 7, 7, 7, 7, 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: [22, 17, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 22, 43, 43, 80, 117, 201, 201, 201, 201, 201, 22, 22, 22, 17, 17, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 80, 80, 201] 201 rigid atoms, others: [43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 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]) total number of confs: 536 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: REAL300025241209 none CN(CC1CCCN1C(=O)C1=CC(N)=CC=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 3, 7, 6, 7, 7, 7, 7, 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: [102, 91, 102, 133, 135, 135, 135, 135, 135, 184, 184, 201, 201, 201, 201, 201, 201, 39, 91, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 102, 133, 133, 135, 135, 135, 135, 135, 135, 135, 201, 201, 201, 201, 201, 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: 735 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: REAL300025241209 none CN(CC1CCCN1C(=O)C1=CC(N)=CC=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 3, 7, 6, 7, 7, 7, 7, 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, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 7, 12, 12, 27, 48, 135, 135, 135, 135, 135, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 27, 27, 135] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 284 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241209 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241209 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241209/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241209 Building REAL300025241210 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241210' /scratch/stefan/7787021/working/building/REAL300025241210 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241210 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241210/0 /scratch/stefan/7787021/working/building/REAL300025241210 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/64 `/scratch/stefan/7787021/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1OCCC1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241210.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241210 none CCC1OCCC1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 7, 7, 19, 19, 54, 89, 199, 199, 199, 199, 199, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 54, 54, 199] 201 rigid atoms, others: [43, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 446 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241210 none CCC1OCCC1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 200, 199, 200, 199, 199, 199, 199, 192, 158, 101, 158, 31, 101, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 199, 199, 199, 199, 199, 192, 192, 158, 158, 158, 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: 723 number of broken/clashed sets: 85 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241210 none CCC1OCCC1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 4, 4, 5, 5, 5, 5, 5, 11, 14, 14, 32, 32, 78, 112, 201, 201, 201, 201, 201, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 11, 11, 14, 14, 14, 78, 78, 201] 201 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: 519 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241210 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241210 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241210/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241210 Building REAL300025241211 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241211' /scratch/stefan/7787021/working/building/REAL300025241211 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300025241211 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241211/0 /scratch/stefan/7787021/working/building/REAL300025241211 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/65 `/scratch/stefan/7787021/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C[N@H+](C)C1CC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241211.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241211 none CN(CC1CCCN1C(=O)C[N@H+](C)C1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 9, 9, 9, 9, 9, 8, 6, 8, 3, 1, 3, 3, 1, 1, 1, 10, 10, 10, 10, 11, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 9, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 10, 10, 12] 12 rigid atoms, others: [48, 11, 44, 45, 14, 15, 16, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 49, 50, 51]) total number of confs: 45 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: REAL300025241211 none CN(CC1CCCN1C(=O)C[N@H+](C)C1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 1] 12 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: 33 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: REAL300025241211 none CN(CC1CCCN1C(=O)C[N@H+](C)C1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 8, 8, 8, 9, 9, 5, 6, 6, 6, 7, 11, 11, 11, 11, 11, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 9, 9, 9, 9, 9, 6, 6, 11] 12 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 60 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241211 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241211/1 /scratch/stefan/7787021/working/building/REAL300025241211 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/66 `/scratch/stefan/7787021/working/3D/66' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C[N@@H+](C)C1CC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241211.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241211/1/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: REAL300025241211 none CN(CC1CCCN1C(=O)C[N@@H+](C)C1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 8, 8, 8, 8, 8, 8, 5, 8, 2, 1, 2, 2, 1, 1, 1, 9, 9, 9, 9, 10, 12, 12, 12, 12, 12, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 8, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 9, 9, 12] 12 rigid atoms, others: [48, 11, 44, 45, 14, 15, 16, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 49, 50, 51]) total number of confs: 48 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: REAL300025241211 none CN(CC1CCCN1C(=O)C[N@@H+](C)C1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 12, 10, 10, 9, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 10, 10, 1] 12 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: 28 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: REAL300025241211 none CN(CC1CCCN1C(=O)C[N@@H+](C)C1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 7, 7, 7, 8, 8, 4, 4, 4, 4, 5, 10, 10, 10, 10, 10, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 8, 8, 8, 8, 8, 4, 4, 10] 12 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241211 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `2' /scratch/stefan/7787021/working/building/REAL300025241211/2 /scratch/stefan/7787021/working/building/REAL300025241211 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 2 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/67 `/scratch/stefan/7787021/working/3D/67' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CN(C)C1CC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241211.mol2' -> `2.mol2' `temp.mol2' -> `REAL300025241211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241211/2/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: REAL300025241211 none CN(CC1CCCN1C(=O)CN(C)C1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 5, 4, 5, 2, 1, 2, 1, 1, 1, 8, 10, 10, 15, 17, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 15, 15, 24] 24 rigid atoms, others: [45, 11, 43, 44, 13, 14, 15, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50]) total number of confs: 74 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: REAL300025241211 none CN(CC1CCCN1C(=O)CN(C)C1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 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: [16, 16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 24, 24, 24, 24, 24, 16, 16, 9, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 16, 16, 1] 24 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: 95 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: REAL300025241211 none CN(CC1CCCN1C(=O)CN(C)C1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 7, 7, 7, 7, 3, 4, 4, 7, 9, 16, 16, 16, 16, 16, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16] 24 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 62 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241211 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241211 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241211/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241211/1.* 2: /scratch/stefan/7787021/working/building/REAL300025241211/2.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241211 Building REAL300025241212 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241212' /scratch/stefan/7787021/working/building/REAL300025241212 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241212 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241212/0 /scratch/stefan/7787021/working/building/REAL300025241212 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/68 `/scratch/stefan/7787021/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC1=CC=CN1C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241212.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241212 none CN(CC1CCCN1C(=O)CC1=CC=CN1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 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 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, 4, 4, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 8, 9, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 2, 2, 2, 8, 8, 10] 10 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 15, 16, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48, 49]) total number of confs: 39 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: REAL300025241212 none CN(CC1CCCN1C(=O)CC1=CC=CN1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 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 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 8, 8, 7, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 8, 8, 1] 10 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: 26 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: REAL300025241212 none CN(CC1CCCN1C(=O)CC1=CC=CN1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 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 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 2, 3, 3, 6, 7, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 8] 10 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 40 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241212 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241212 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241212/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241212 Building REAL300025241213 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241213' /scratch/stefan/7787021/working/building/REAL300025241213 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241213 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241213/0 /scratch/stefan/7787021/working/building/REAL300025241213 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/69 `/scratch/stefan/7787021/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CCOC1CC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241213.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241213 none CN(CC1CCCN1C(=O)CCOC1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 27, 27, 27, 27, 27, 27, 14, 27, 14, 5, 1, 1, 1, 1, 54, 83, 83, 130, 153, 201, 201, 201, 201, 201, 54, 54, 54, 45, 45, 27, 27, 27, 27, 27, 27, 27, 14, 14, 14, 14, 1, 1, 1, 1, 1, 130, 130, 201] 201 rigid atoms, others: [45, 44, 42, 43, 12, 13, 14, 15, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49]) total number of confs: 679 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241213 none CN(CC1CCCN1C(=O)CCOC1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 67, 86, 99, 99, 99, 99, 99, 99, 99, 134, 134, 193, 201, 201, 19, 46, 12, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 86, 86, 99, 99, 99, 99, 99, 99, 99, 134, 134, 134, 134, 201, 201, 201, 201, 201, 19, 19, 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: 679 number of broken/clashed sets: 70 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241213 none CN(CC1CCCN1C(=O)CCOC1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 15, 27, 27, 6, 11, 11, 30, 41, 99, 99, 99, 99, 99, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 27, 27, 27, 27, 27, 30, 30, 99] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 292 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241213 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241213 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241213/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241213 Building REAL300025241214 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241214' /scratch/stefan/7787021/working/building/REAL300025241214 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241214 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241214/0 /scratch/stefan/7787021/working/building/REAL300025241214 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/70 `/scratch/stefan/7787021/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CCCCCO)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241214.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241214 none CN(CC1CCCN1C(=O)CCCCCO)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 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, 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: [42, 32, 42, 59, 59, 59, 59, 59, 59, 59, 59, 169, 201, 201, 201, 201, 21, 32, 13, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 59, 59, 59, 59, 59, 59, 59, 59, 59, 169, 169, 201, 201, 201, 201, 201, 201, 201, 201, 603, 21, 21, 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: 1479 number of broken/clashed sets: 450 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241214 none CN(CC1CCCN1C(=O)CCCCCO)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 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, 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, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 10, 10, 10, 18, 3, 4, 4, 9, 14, 59, 59, 59, 59, 59, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 10, 10, 10, 10, 10, 10, 18, 18, 54, 9, 9, 59] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 236 number of broken/clashed sets: 450 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241214 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241214 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241214/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241214 Building REAL300025241215 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241215' /scratch/stefan/7787021/working/building/REAL300025241215 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241215 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241215/0 /scratch/stefan/7787021/working/building/REAL300025241215 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/71 `/scratch/stefan/7787021/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1C[C@@H]1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241215.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241215 none COC(=O)[C@@H]1C[C@@H]1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 12, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 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: [7, 7, 5, 7, 5, 5, 5, 3, 5, 1, 3, 1, 1, 1, 1, 1, 1, 4, 7, 7, 16, 16, 45, 71, 151, 151, 151, 151, 151, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 45, 45, 151] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 366 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: REAL300025241215 none COC(=O)[C@@H]1C[C@@H]1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 12, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 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: [201, 201, 173, 201, 173, 173, 173, 151, 173, 151, 151, 151, 151, 151, 151, 150, 124, 90, 124, 27, 90, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 173, 173, 151, 151, 151, 151, 151, 151, 151, 150, 150, 124, 124, 124, 27, 27, 1] 201 rigid atoms, others: [48, 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]) total number of confs: 731 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: REAL300025241215 none COC(=O)[C@@H]1C[C@@H]1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 12, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 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: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 9, 11, 11, 28, 28, 66, 93, 173, 173, 173, 173, 173, 4, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 9, 9, 11, 11, 11, 66, 66, 173] 201 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9] set([0, 1, 3, 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: 459 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241215 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241215 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241215/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241215 Building REAL300025241216 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241216' /scratch/stefan/7787021/working/building/REAL300025241216 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241216 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241216/0 /scratch/stefan/7787021/working/building/REAL300025241216 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/72 `/scratch/stefan/7787021/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CON=C1CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241216.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241216 none CC1=CON=C1CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 7, 7, 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: [9, 9, 9, 9, 9, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 6, 6, 13, 13, 35, 58, 141, 141, 141, 141, 141, 9, 9, 9, 9, 8, 8, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 35, 35, 141] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 325 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: REAL300025241216 none CC1=CON=C1CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 7, 7, 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: [201, 201, 201, 201, 201, 201, 141, 141, 141, 141, 141, 141, 141, 135, 108, 74, 108, 29, 74, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 141, 141, 141, 141, 141, 141, 141, 135, 135, 108, 108, 108, 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: 837 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: REAL300025241216 none CC1=CON=C1CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 7, 7, 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, 1, 1, 1, 5, 8, 8, 9, 9, 9, 9, 9, 14, 16, 16, 30, 30, 73, 111, 201, 201, 201, 201, 201, 2, 2, 2, 1, 5, 5, 9, 9, 9, 9, 9, 9, 9, 14, 14, 16, 16, 16, 73, 73, 201] 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: 530 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241216 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241216 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241216/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241216 Building REAL300025241217 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241217' /scratch/stefan/7787021/working/building/REAL300025241217 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241217 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241217/0 /scratch/stefan/7787021/working/building/REAL300025241217 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/73 `/scratch/stefan/7787021/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1=CC=CC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=C1) `REAL300025241217.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241217 none C#CC1=CC=CC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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: [7, 7, 7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 5, 5, 13, 13, 33, 52, 130, 130, 130, 130, 130, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 33, 33, 130, 7] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 289 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241217 none C#CC1=CC=CC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 201, 201, 201, 201, 131, 130, 131, 130, 130, 130, 130, 119, 106, 72, 106, 25, 72, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 130, 130, 130, 130, 130, 130, 130, 119, 119, 106, 106, 106, 25, 25, 1, 201] 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]) total number of confs: 588 number of broken/clashed sets: 77 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241217 none C#CC1=CC=CC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 13, 17, 17, 37, 37, 88, 122, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 13, 13, 17, 17, 17, 88, 88, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 47, 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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 554 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241217 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241217 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241217/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241217 Building REAL300025241218 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241218' /scratch/stefan/7787021/working/building/REAL300025241218 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241218 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241218/0 /scratch/stefan/7787021/working/building/REAL300025241218 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/74 `/scratch/stefan/7787021/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=N1) `REAL300025241218.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241218 none CCC1=NOC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 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: [20, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 4, 4, 5, 5, 10, 17, 91, 91, 91, 91, 91, 6, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 10, 10, 91] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 211 number of broken/clashed sets: 159 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241218 none CCC1=NOC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 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: [201, 150, 150, 150, 150, 123, 91, 123, 91, 91, 91, 91, 89, 58, 49, 58, 31, 49, 13, 1, 1, 1, 1, 1, 1, 1, 150, 201, 201, 201, 201, 201, 91, 91, 91, 91, 91, 91, 91, 89, 89, 58, 58, 58, 31, 31, 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: 878 number of broken/clashed sets: 159 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241218 none CCC1=NOC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 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: [7, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 11, 13, 13, 15, 15, 34, 55, 150, 150, 150, 150, 150, 1, 8, 8, 8, 7, 7, 6, 6, 6, 6, 6, 6, 6, 11, 11, 13, 13, 13, 34, 34, 150] 201 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: 354 number of broken/clashed sets: 159 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241218 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241218 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241218/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241218 Building REAL300025241219 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241219' /scratch/stefan/7787021/working/building/REAL300025241219 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241219 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241219/0 /scratch/stefan/7787021/working/building/REAL300025241219 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/75 `/scratch/stefan/7787021/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)C[NH+](C)C) `REAL300025241219.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241219 none CC(CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 48, 48, 48, 48, 48, 48, 48, 47, 47, 43, 47, 25, 43, 12, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 48, 48, 48, 48, 48, 48, 48, 47, 47, 47, 47, 47, 25, 25, 1, 55, 55, 55, 55, 55, 55, 55, 55] 55 rigid atoms, others: [48, 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, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 198 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: REAL300025241219 none CC(CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [9, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 5, 5, 6, 6, 19, 27, 48, 48, 48, 48, 48, 9, 11, 11, 11, 11, 9, 9, 9, 9, 7, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 19, 19, 48, 11, 11, 11, 11, 11, 11, 11, 11] 55 rigid atoms, others: [34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 40, 35, 38, 37] set([0, 1, 2, 4, 11, 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, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 169 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241219 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241219 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241219/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241219 Building REAL300025241220 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241220' /scratch/stefan/7787021/working/building/REAL300025241220 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241220 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241220/0 /scratch/stefan/7787021/working/building/REAL300025241220 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/76 `/scratch/stefan/7787021/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CN1C=C(N)C=N1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241220.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241220 none CN(CC1CCCN1C(=O)CN1C=C(N)C=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 13, 6, 6, 6, 6, 6, 6, 5, 6, 1, 1, 1, 1, 1, 1, 1, 14, 31, 31, 78, 112, 201, 201, 201, 201, 201, 14, 14, 14, 13, 13, 6, 6, 6, 6, 6, 6, 6, 5, 5, 1, 1, 1, 1, 78, 78, 201] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 15, 16, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47]) total number of confs: 561 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241220 none CN(CC1CCCN1C(=O)CN1C=C(N)C=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 66, 97, 113, 121, 121, 121, 121, 121, 121, 121, 201, 201, 201, 201, 201, 201, 27, 66, 12, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 113, 113, 121, 121, 121, 121, 121, 121, 121, 201, 201, 201, 201, 201, 201, 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: 843 number of broken/clashed sets: 77 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241220 none CN(CC1CCCN1C(=O)CN1C=C(N)C=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [5, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 6, 6, 6, 6, 6, 5, 10, 10, 29, 43, 121, 121, 121, 121, 121, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 29, 29, 121] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 274 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241220 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241220 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241220/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241220 Building REAL300025241221 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241221' /scratch/stefan/7787021/working/building/REAL300025241221 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241221 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241221/0 /scratch/stefan/7787021/working/building/REAL300025241221 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/77 `/scratch/stefan/7787021/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCO)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241221.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241221 none CC(CCO)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 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, 198, 201, 201, 201, 198, 198, 198, 198, 198, 198, 189, 156, 99, 156, 30, 99, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 603, 198, 198, 198, 198, 198, 198, 198, 189, 189, 156, 156, 156, 30, 30, 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: 1339 number of broken/clashed sets: 269 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241221 none CC(CCO)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 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, 2, 3, 5, 6, 1, 2, 1, 1, 1, 1, 1, 1, 4, 6, 6, 14, 14, 49, 80, 198, 198, 198, 198, 198, 3, 3, 3, 3, 5, 5, 6, 6, 18, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 49, 49, 198] 603 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 458 number of broken/clashed sets: 269 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241221 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241221 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241221/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241221 Building REAL300025241222 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241222' /scratch/stefan/7787021/working/building/REAL300025241222 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241222 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241222/0 /scratch/stefan/7787021/working/building/REAL300025241222 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/78 `/scratch/stefan/7787021/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C(F)=CC1CC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241222.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241222 none CN(CC1CCCN1C(=O)C(F)=CC1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 15, 1, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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] 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, 4, 4, 4, 4, 3, 4, 3, 3, 1, 1, 1, 1, 4, 5, 5, 7, 9, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 7, 7, 10] 10 rigid atoms, others: [39, 40, 41, 42, 43, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46]) total number of confs: 30 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: REAL300025241222 none CN(CC1CCCN1C(=O)C(F)=CC1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 15, 1, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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] 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: [8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 10, 10, 8, 8, 7, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 10, 10, 10, 10, 10, 8, 8, 1] 10 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: 22 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: REAL300025241222 none CN(CC1CCCN1C(=O)C(F)=CC1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 15, 1, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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] 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: [2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 4, 4, 2, 3, 3, 5, 6, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 5, 5, 8] 10 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 38 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241222 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241222 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241222/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241222 Building REAL300025241223 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241223' /scratch/stefan/7787021/working/building/REAL300025241223 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241223 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241223/0 /scratch/stefan/7787021/working/building/REAL300025241223 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/79 `/scratch/stefan/7787021/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC1CC(F)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241223.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241223 none CN(CC1CCCN1C(=O)CC1CC(F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 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: [11, 11, 10, 10, 10, 10, 10, 10, 5, 10, 1, 1, 1, 1, 1, 1, 11, 16, 16, 27, 28, 32, 32, 32, 32, 32, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 27, 27, 32] 32 rigid atoms, others: [45, 43, 40, 41, 10, 11, 12, 13, 14, 15, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 119 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: REAL300025241223 none CN(CC1CCCN1C(=O)CC1CC(F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 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: [12, 12, 12, 12, 12, 12, 12, 12, 12, 13, 13, 26, 32, 32, 32, 32, 12, 12, 9, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 32, 32, 32, 32, 32, 32, 12, 12, 1] 32 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: 116 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: REAL300025241223 none CN(CC1CCCN1C(=O)CC1CC(F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 10, 10, 10, 10, 3, 4, 4, 7, 9, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 7, 7, 12] 32 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 69 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241223 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241223 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241223/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241223 Building REAL300025241224 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241224' /scratch/stefan/7787021/working/building/REAL300025241224 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241224 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241224/0 /scratch/stefan/7787021/working/building/REAL300025241224 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/80 `/scratch/stefan/7787021/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C(F)CC1CCC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241224.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241224 none CN(CC1CCCN1C(=O)C(F)CC1CCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 14, 6, 14, 4, 6, 1, 1, 1, 1, 1, 26, 39, 39, 78, 115, 201, 201, 201, 201, 201, 26, 26, 26, 25, 25, 14, 14, 14, 14, 14, 14, 14, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 78, 78, 201] 201 rigid atoms, others: [48, 45, 44, 42, 43, 12, 13, 14, 15, 16, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 49, 50, 51]) total number of confs: 551 number of broken/clashed sets: 93 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241224 none CN(CC1CCCN1C(=O)C(F)CC1CCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 60, 87, 96, 100, 100, 100, 100, 100, 100, 100, 111, 111, 111, 201, 201, 201, 23, 59, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 96, 96, 100, 100, 100, 100, 100, 100, 100, 111, 111, 111, 201, 201, 201, 201, 201, 201, 201, 23, 23, 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: 759 number of broken/clashed sets: 93 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241224 none CN(CC1CCCN1C(=O)C(F)CC1CCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 1, 1, 2, 2, 6, 6, 7, 14, 14, 14, 5, 9, 9, 24, 40, 100, 100, 100, 100, 100, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 14, 14, 14, 14, 14, 14, 14, 24, 24, 100] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 262 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241224 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241224 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241224/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241224 Building REAL300025241225 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241225' /scratch/stefan/7787021/working/building/REAL300025241225 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241225 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241225/0 /scratch/stefan/7787021/working/building/REAL300025241225 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/81 `/scratch/stefan/7787021/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)[C@H](O)CF)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241225.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241225 none CN(CC1CCCN1C(=O)[C@H](O)CF)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 15, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 6, 7, 7, 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 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 14, 14, 14, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 42, 14, 14, 11, 11, 1] 42 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: 87 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: REAL300025241225 none CN(CC1CCCN1C(=O)[C@H](O)CF)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 15, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 6, 7, 7, 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 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 3, 4, 4, 7, 9, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 12, 4, 4, 7, 7, 11] 42 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 59 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241225 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241225 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241225/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241225 Building REAL300025241226 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241226' /scratch/stefan/7787021/working/building/REAL300025241226 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241226 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241226/0 /scratch/stefan/7787021/working/building/REAL300025241226 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/82 `/scratch/stefan/7787021/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C)C=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025241226.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241226 none CCC1(C)C=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 5, 5, 10, 10, 25, 40, 105, 105, 105, 105, 105, 10, 12, 12, 12, 12, 12, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 25, 25, 105, 10, 10] 201 rigid atoms, others: [36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 251 number of broken/clashed sets: 114 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241226 none CCC1(C)C=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 124, 105, 124, 105, 105, 105, 105, 99, 86, 61, 86, 24, 60, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 105, 105, 105, 105, 105, 105, 105, 99, 99, 86, 86, 86, 24, 24, 1, 201, 201] 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]) total number of confs: 555 number of broken/clashed sets: 114 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241226 none CCC1(C)C=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 19, 20, 20, 34, 34, 73, 103, 201, 201, 201, 201, 201, 1, 3, 3, 3, 2, 2, 2, 2, 2, 1, 10, 10, 10, 10, 10, 10, 10, 19, 19, 20, 20, 20, 73, 73, 201, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 52, 26, 51] 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 567 number of broken/clashed sets: 114 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241226 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241226 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241226/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241226 Building REAL300025241227 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241227' /scratch/stefan/7787021/working/building/REAL300025241227 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241227 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241227/0 /scratch/stefan/7787021/working/building/REAL300025241227 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/83 `/scratch/stefan/7787021/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C)CC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025241227.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241227 none CCC1(C)CC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 4, 4, 9, 9, 27, 44, 124, 124, 124, 124, 124, 6, 10, 10, 10, 10, 10, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 27, 27, 124, 6, 6] 201 rigid atoms, others: [43, 6, 38, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 286 number of broken/clashed sets: 66 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241227 none CCC1(C)CC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 124, 124, 124, 124, 124, 124, 124, 114, 96, 70, 96, 27, 69, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 124, 124, 124, 124, 124, 124, 124, 114, 114, 96, 96, 96, 27, 27, 1, 201, 201] 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]) total number of confs: 726 number of broken/clashed sets: 66 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241227 none CCC1(C)CC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 6, 6, 11, 13, 13, 29, 29, 62, 93, 201, 201, 201, 201, 201, 1, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 11, 11, 13, 13, 13, 62, 62, 201, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 53, 54, 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, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 490 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241227 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241227 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241227/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241227 Building REAL300025241228 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241228' /scratch/stefan/7787021/working/building/REAL300025241228 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241228 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241228/0 /scratch/stefan/7787021/working/building/REAL300025241228 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/84 `/scratch/stefan/7787021/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=NC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=N1) `REAL300025241228.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241228 none CCN1C=NC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=N1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 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, 7, 7, 7, 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: [13, 7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 9, 16, 76, 76, 76, 76, 76, 7, 13, 13, 13, 13, 13, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 76] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 172 number of broken/clashed sets: 157 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241228 none CCN1C=NC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=N1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 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, 7, 7, 7, 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: [201, 143, 143, 143, 143, 98, 76, 98, 76, 76, 76, 76, 76, 48, 42, 48, 28, 41, 13, 1, 1, 1, 1, 1, 1, 1, 143, 201, 201, 201, 201, 201, 143, 76, 76, 76, 76, 76, 76, 76, 76, 76, 48, 48, 48, 28, 28, 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: 846 number of broken/clashed sets: 157 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241228 none CCN1C=NC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=N1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 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, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 12, 12, 12, 14, 14, 33, 51, 143, 143, 143, 143, 143, 1, 3, 3, 3, 3, 3, 1, 7, 7, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 33, 33, 143] 201 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: 325 number of broken/clashed sets: 157 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241228 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241228 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241228/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241228 Building REAL300025241229 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241229' /scratch/stefan/7787021/working/building/REAL300025241229 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241229 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241229/0 /scratch/stefan/7787021/working/building/REAL300025241229 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/85 `/scratch/stefan/7787021/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)(O)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241229.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241229 none CCCC(C)(O)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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, 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, 181, 181, 181, 181, 144, 144, 144, 144, 144, 144, 144, 137, 119, 84, 119, 29, 84, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 181, 181, 181, 543, 181, 181, 144, 144, 144, 144, 144, 144, 144, 137, 137, 119, 119, 119, 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: 1366 number of broken/clashed sets: 312 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241229 none CCCC(C)(O)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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, 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, 7, 6, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 26, 47, 144, 144, 144, 144, 144, 16, 16, 16, 16, 16, 16, 16, 7, 7, 7, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 26, 26, 144] 603 rigid atoms, others: [45, 43, 7, 40, 9, 10, 11, 12, 13, 14, 44, 46, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 357 number of broken/clashed sets: 312 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241229 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241229 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241229/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241229 Building REAL300025241230 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241230' /scratch/stefan/7787021/working/building/REAL300025241230 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241230 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241230/0 /scratch/stefan/7787021/working/building/REAL300025241230 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/86 `/scratch/stefan/7787021/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CC=C(C#N)O1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241230.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241230 none CN(CC1CCCN1C(=O)C1=CC=C(C#N)O1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.1', 'N.1', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 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 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [34, 24, 13, 13, 13, 13, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 34, 66, 66, 83, 118, 189, 189, 189, 189, 189, 34, 34, 34, 24, 24, 13, 13, 13, 13, 13, 13, 13, 1, 1, 83, 83, 189] 189 rigid atoms, others: [39, 8, 10, 11, 12, 13, 14, 15, 16, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 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]) total number of confs: 507 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: REAL300025241230 none CN(CC1CCCN1C(=O)C1=CC=C(C#N)O1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.1', 'N.1', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 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 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [96, 84, 96, 130, 136, 136, 136, 136, 136, 164, 164, 189, 189, 189, 189, 189, 189, 38, 84, 13, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 130, 130, 136, 136, 136, 136, 136, 136, 136, 189, 189, 38, 38, 1] 189 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: 683 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: REAL300025241230 none CN(CC1CCCN1C(=O)C1=CC=C(C#N)O1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.1', 'N.1', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 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 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 13, 13, 13, 10, 19, 19, 28, 48, 136, 136, 136, 136, 136, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 13, 13, 28, 28, 136] 189 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43]) total number of confs: 279 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241230 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241230 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241230/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241230 Building REAL300025241231 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241231' /scratch/stefan/7787021/working/building/REAL300025241231 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241231 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241231/0 /scratch/stefan/7787021/working/building/REAL300025241231 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/87 `/scratch/stefan/7787021/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC1=CC=CC=N1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241231.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241231 none CN(CC1CCCN1C(=O)CC1=CC=CC=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 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, 15, 9, 9, 9, 9, 9, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 17, 35, 35, 78, 107, 201, 201, 201, 201, 201, 17, 17, 17, 15, 15, 9, 9, 9, 9, 9, 9, 9, 5, 5, 1, 1, 1, 1, 78, 78, 201] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 15, 16, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47]) total number of confs: 542 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241231 none CN(CC1CCCN1C(=O)CC1=CC=CC=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 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, 70, 102, 129, 138, 138, 138, 138, 138, 139, 139, 201, 201, 201, 201, 201, 201, 26, 70, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 102, 129, 129, 138, 138, 138, 138, 138, 138, 138, 201, 201, 201, 201, 201, 201, 26, 26, 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: 883 number of broken/clashed sets: 81 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241231 none CN(CC1CCCN1C(=O)CC1=CC=CC=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 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: [5, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 9, 9, 9, 9, 9, 5, 13, 13, 33, 50, 138, 138, 138, 138, 138, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 9, 9, 33, 33, 138] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 314 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241231 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241231 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241231/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241231 Building REAL300025241232 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241232' /scratch/stefan/7787021/working/building/REAL300025241232 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241232 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241232/0 /scratch/stefan/7787021/working/building/REAL300025241232 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/88 `/scratch/stefan/7787021/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C(O)C1CC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241232.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241232 none CN(CC1CCCN1C(=O)C(O)C1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 9, 9, 9, 9, 9, 8, 6, 8, 1, 6, 1, 1, 1, 11, 13, 13, 19, 22, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 9, 6, 18, 1, 1, 1, 1, 1, 19, 19, 28] 84 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]) total number of confs: 111 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: REAL300025241232 none CN(CC1CCCN1C(=O)C(O)C1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 23, 23, 28, 28, 16, 16, 10, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 23, 69, 28, 28, 28, 28, 28, 16, 16, 1] 84 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: 170 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: REAL300025241232 none CN(CC1CCCN1C(=O)C(O)C1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [4, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 9, 9, 4, 5, 5, 8, 10, 16, 16, 16, 16, 16, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 15, 9, 9, 9, 9, 9, 8, 8, 16] 84 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 88 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241232 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241232 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241232/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241232 Building REAL300025241233 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241233' /scratch/stefan/7787021/working/building/REAL300025241233 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241233 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241233/0 /scratch/stefan/7787021/working/building/REAL300025241233 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/89 `/scratch/stefan/7787021/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CN1C=NN=C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241233.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241233 none CN(CC1CCCN1C(=O)CN1C=NN=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 8, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 15, 15, 15, 15, 15, 13, 7, 13, 1, 1, 1, 1, 1, 1, 18, 19, 19, 25, 30, 39, 39, 39, 39, 39, 18, 18, 18, 18, 18, 15, 15, 15, 15, 15, 15, 15, 7, 7, 1, 1, 25, 25, 39] 39 rigid atoms, others: [40, 41, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 124 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: REAL300025241233 none CN(CC1CCCN1C(=O)CN1C=NN=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 8, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 20, 20, 38, 38, 38, 38, 38, 19, 19, 10, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 38, 38, 38, 38, 19, 19, 1] 38 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: 156 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: REAL300025241233 none CN(CC1CCCN1C(=O)CN1C=NN=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 8, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 12, 12, 12, 12, 4, 5, 5, 8, 11, 19, 19, 19, 19, 19, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 12, 12, 8, 8, 19] 38 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 85 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241233 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241233 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241233/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241233 Building REAL300025241234 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241234' /scratch/stefan/7787021/working/building/REAL300025241234 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241234 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241234/0 /scratch/stefan/7787021/working/building/REAL300025241234 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/90 `/scratch/stefan/7787021/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241234.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241234 none C=C(C)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1] 20 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: 69 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: REAL300025241234 none C=C(C)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 6, 8, 10, 10, 10, 10, 10, 7, 7, 7, 7, 7, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 10] 20 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 53 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241234 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241234 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241234/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241234 Building REAL300025241235 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241235' /scratch/stefan/7787021/working/building/REAL300025241235 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241235 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241235/0 /scratch/stefan/7787021/working/building/REAL300025241235 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/91 `/scratch/stefan/7787021/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CCC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)CC1) `REAL300025241235.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241235 none CC1=CCC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)CC1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 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, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 5, 5, 14, 14, 38, 59, 162, 162, 162, 162, 162, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 38, 38, 162, 3, 3, 3, 3] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 342 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241235 none CC1=CCC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)CC1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 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, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 162, 162, 162, 162, 162, 162, 162, 148, 120, 78, 120, 28, 78, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 162, 162, 162, 162, 162, 162, 148, 148, 120, 120, 120, 28, 28, 1, 201, 201, 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]) total number of confs: 756 number of broken/clashed sets: 67 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241235 none CC1=CCC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)CC1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 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, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 3, 3, 3, 3, 7, 9, 9, 26, 26, 69, 102, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 7, 7, 9, 9, 9, 69, 69, 201, 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: 495 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241235 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241235 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241235/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241235 Building REAL300025241236 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241236' /scratch/stefan/7787021/working/building/REAL300025241236 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241236 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241236/0 /scratch/stefan/7787021/working/building/REAL300025241236 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/92 `/scratch/stefan/7787021/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241236.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241236 none CCSCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 14, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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: [201, 201, 189, 150, 150, 150, 150, 150, 150, 150, 146, 110, 76, 110, 30, 76, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 189, 189, 150, 150, 150, 150, 150, 150, 150, 146, 146, 110, 110, 110, 30, 30, 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: 842 number of broken/clashed sets: 129 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241236 none CCSCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 14, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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: [11, 8, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 5, 5, 8, 8, 23, 38, 150, 150, 150, 150, 150, 11, 11, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 23, 23, 150] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 292 number of broken/clashed sets: 129 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241236 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241236 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241236/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241236 Building REAL300025241237 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241237' /scratch/stefan/7787021/working/building/REAL300025241237 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241237 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241237/0 /scratch/stefan/7787021/working/building/REAL300025241237 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/93 `/scratch/stefan/7787021/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)OCCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241237.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241237 none CC(=O)OCCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 11, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 5, 3, 7, 7, 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: [201, 201, 201, 117, 117, 53, 53, 53, 53, 53, 53, 53, 53, 39, 32, 39, 23, 32, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 117, 117, 117, 117, 53, 53, 53, 53, 53, 53, 53, 53, 53, 39, 39, 39, 23, 23, 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: 631 number of broken/clashed sets: 157 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241237 none CC(=O)OCCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 11, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 5, 3, 7, 7, 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: [13, 13, 13, 6, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 9, 15, 53, 53, 53, 53, 53, 13, 13, 13, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 53] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 135 number of broken/clashed sets: 157 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241237 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241237 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241237/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241237 Building REAL300025241238 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241238' /scratch/stefan/7787021/working/building/REAL300025241238 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241238 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241238/0 /scratch/stefan/7787021/working/building/REAL300025241238 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/94 `/scratch/stefan/7787021/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(C)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241238.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241238 none CC(C)=C(C)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 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: [201, 201, 201, 108, 201, 108, 108, 108, 108, 108, 108, 108, 87, 79, 87, 34, 79, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 108, 108, 108, 108, 108, 108, 108, 108, 108, 87, 87, 87, 34, 34, 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: 785 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: REAL300025241238 none CC(C)=C(C)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 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: [3, 3, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 4, 6, 6, 14, 14, 34, 54, 108, 108, 108, 108, 108, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 34, 34, 108] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 269 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241238 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241238 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241238/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241238 Building REAL300025241239 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241239' /scratch/stefan/7787021/working/building/REAL300025241239 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241239 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241239/0 /scratch/stefan/7787021/working/building/REAL300025241239 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/95 `/scratch/stefan/7787021/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)C=NS1) `REAL300025241239.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241239 none CC1=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)C=NS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', '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, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 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: [12, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 4, 6, 6, 11, 11, 23, 40, 114, 114, 114, 114, 114, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 23, 23, 114, 12] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 35, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 249 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: REAL300025241239 none CC1=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)C=NS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', '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, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 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: [201, 201, 137, 114, 137, 114, 114, 114, 114, 110, 86, 82, 86, 36, 82, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 114, 114, 114, 114, 114, 114, 114, 110, 110, 86, 86, 86, 36, 36, 1, 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]) total number of confs: 643 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: REAL300025241239 none CC1=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)C=NS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', '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, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 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, 6, 6, 12, 12, 12, 12, 12, 21, 26, 26, 47, 47, 86, 121, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 21, 21, 26, 26, 26, 86, 86, 201, 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: 571 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241239 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241239 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241239/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241239 Building REAL300025241240 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241240' /scratch/stefan/7787021/working/building/REAL300025241240 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241240 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241240/0 /scratch/stefan/7787021/working/building/REAL300025241240 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/96 `/scratch/stefan/7787021/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CC=NC=C1[O-])C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241240.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241240 none CN(CC1CCCN1C(=O)C1=CC=NC=C1[O-])C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 6, 7, 7, 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: [22, 15, 9, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 22, 46, 46, 80, 135, 201, 201, 201, 201, 201, 22, 22, 22, 15, 15, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 80, 80, 201] 201 rigid atoms, others: [39, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44]) total number of confs: 521 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: REAL300025241240 none CN(CC1CCCN1C(=O)C1=CC=NC=C1[O-])C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 6, 7, 7, 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: [118, 93, 118, 140, 142, 142, 142, 142, 142, 185, 185, 201, 201, 201, 201, 201, 201, 37, 93, 13, 1, 1, 1, 1, 1, 1, 1, 118, 118, 118, 140, 140, 142, 142, 142, 142, 142, 142, 142, 201, 201, 201, 37, 37, 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: 720 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: REAL300025241240 none CN(CC1CCCN1C(=O)C1=CC=NC=C1[O-])C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 6, 7, 7, 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: [8, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 8, 18, 18, 41, 66, 142, 142, 142, 142, 142, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 41, 41, 142] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44]) total number of confs: 322 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241240 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241240/1 /scratch/stefan/7787021/working/building/REAL300025241240 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/97 `/scratch/stefan/7787021/working/3D/97' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CC=NC=C1O)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241240.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241240/1/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: REAL300025241240 none CN(CC1CCCN1C(=O)C1=CC=NC=C1O)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 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] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [25, 17, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 25, 54, 54, 104, 139, 201, 201, 201, 201, 201, 25, 25, 25, 17, 17, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 2, 104, 104, 201] 402 rigid atoms, others: [39, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45]) total number of confs: 591 number of broken/clashed sets: 135 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241240 none CN(CC1CCCN1C(=O)C1=CC=NC=C1O)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 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] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [121, 97, 121, 158, 168, 168, 168, 168, 168, 178, 178, 201, 201, 201, 201, 201, 201, 39, 97, 13, 1, 1, 1, 1, 1, 1, 1, 121, 121, 121, 158, 158, 168, 168, 168, 168, 168, 168, 168, 201, 201, 201, 402, 39, 39, 1] 402 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: 1117 number of broken/clashed sets: 135 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241240 none CN(CC1CCCN1C(=O)C1=CC=NC=C1O)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 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] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 9, 22, 22, 52, 83, 168, 168, 168, 168, 168, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 16, 52, 52, 168] 402 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 412 number of broken/clashed sets: 135 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241240 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241240 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241240/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241240/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241240 Building REAL300025241241 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241241' /scratch/stefan/7787021/working/building/REAL300025241241 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241241 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241241/0 /scratch/stefan/7787021/working/building/REAL300025241241 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/98 `/scratch/stefan/7787021/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CCC1(C)N=N1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241241.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241241 none CN(CC1CCCN1C(=O)CCC1(C)N=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 8, 8, 8, 8, 8, 8, 6, 8, 6, 1, 1, 1, 1, 1, 9, 11, 11, 17, 18, 20, 20, 20, 20, 20, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 2, 2, 2, 17, 17, 20] 20 rigid atoms, others: [11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 78 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: REAL300025241241 none CN(CC1CCCN1C(=O)CCC1(C)N=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 18, 20, 20, 20, 11, 11, 9, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 18, 18, 20, 20, 20, 11, 11, 1] 20 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: 69 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: REAL300025241241 none CN(CC1CCCN1C(=O)CCC1(C)N=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 7, 8, 8, 8, 3, 4, 4, 7, 9, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 8, 8, 8, 7, 7, 11] 20 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 63 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241241 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241241 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241241/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241241 Building REAL300025241242 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241242' /scratch/stefan/7787021/working/building/REAL300025241242 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241242 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241242/0 /scratch/stefan/7787021/working/building/REAL300025241242 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/99 `/scratch/stefan/7787021/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CC(=O)[N-]O1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241242.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241242 none CN(CC1CCCN1C(=O)C1=CC(=O)[N-]O1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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: [25, 17, 10, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 25, 50, 50, 79, 118, 201, 201, 201, 201, 201, 25, 25, 25, 17, 17, 10, 10, 10, 10, 10, 10, 10, 1, 79, 79, 201] 201 rigid atoms, others: [38, 8, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 538 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: REAL300025241242 none CN(CC1CCCN1C(=O)C1=CC(=O)[N-]O1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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: [125, 106, 125, 154, 162, 162, 162, 162, 162, 199, 199, 201, 201, 201, 201, 201, 40, 106, 13, 1, 1, 1, 1, 1, 1, 1, 125, 125, 125, 154, 154, 162, 162, 162, 162, 162, 162, 162, 201, 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: 740 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: REAL300025241242 none CN(CC1CCCN1C(=O)C1=CC(=O)[N-]O1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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: [7, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 10, 7, 12, 12, 27, 49, 162, 162, 162, 162, 162, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 27, 27, 162] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41]) total number of confs: 317 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241242 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241242 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241242/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241242 Building REAL300025241243 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241243' /scratch/stefan/7787021/working/building/REAL300025241243 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241243 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241243/0 /scratch/stefan/7787021/working/building/REAL300025241243 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/100 `/scratch/stefan/7787021/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)COC1COC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241243.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241243 none CN(CC1CCCN1C(=O)COC1COC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 15, 15, 15, 15, 15, 14, 12, 14, 4, 1, 1, 1, 1, 1, 16, 20, 20, 32, 37, 47, 47, 47, 47, 47, 16, 16, 16, 16, 16, 15, 15, 15, 15, 15, 15, 15, 12, 12, 1, 1, 1, 1, 1, 32, 32, 47] 47 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47]) total number of confs: 148 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: REAL300025241243 none CN(CC1CCCN1C(=O)COC1COC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 12, 13, 13, 23, 32, 47, 47, 47, 12, 12, 9, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 47, 47, 47, 47, 47, 12, 12, 1] 47 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: 158 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: REAL300025241243 none CN(CC1CCCN1C(=O)COC1COC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 8, 15, 15, 15, 3, 4, 4, 7, 9, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 15, 15, 7, 7, 12] 47 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 82 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241243 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241243 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241243/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241243 Building REAL300025241244 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241244' /scratch/stefan/7787021/working/building/REAL300025241244 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241244 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241244/0 /scratch/stefan/7787021/working/building/REAL300025241244 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/101 `/scratch/stefan/7787021/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@]2(C(=O)N3CCCC3CN(C)C(=O)CSC3=NNC(=O)[N-]3)C[C@H]12) `REAL300025241244.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241244 none C[C@@H]1C[C@]2(C(=O)N3CCCC3CN(C)C(=O)CSC3=NNC(=O)[N-]3)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 5, 8, 5, 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, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 1, 1, 1, 4, 8, 8, 22, 22, 62, 98, 195, 195, 195, 195, 195, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 62, 62, 195, 5, 5] 201 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 460 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241244 none C[C@@H]1C[C@]2(C(=O)N3CCCC3CN(C)C(=O)CSC3=NNC(=O)[N-]3)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 5, 8, 5, 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, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 195, 201, 195, 195, 195, 195, 187, 161, 105, 161, 30, 105, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 195, 195, 195, 195, 195, 195, 195, 187, 187, 161, 161, 161, 30, 30, 1, 201, 201] 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]) total number of confs: 691 number of broken/clashed sets: 92 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241244 none C[C@@H]1C[C@]2(C(=O)N3CCCC3CN(C)C(=O)CSC3=NNC(=O)[N-]3)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 5, 8, 5, 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, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 2, 2, 5, 5, 5, 5, 5, 10, 13, 13, 30, 30, 74, 111, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 5, 5, 5, 5, 5, 5, 5, 10, 10, 13, 13, 13, 74, 74, 201, 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: 509 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241244 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241244 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241244/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241244 Building REAL300025241245 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241245' /scratch/stefan/7787021/working/building/REAL300025241245 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241245 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241245/0 /scratch/stefan/7787021/working/building/REAL300025241245 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/102 `/scratch/stefan/7787021/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241245.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241245 none CNC(=O)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 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: [201, 201, 201, 201, 145, 145, 145, 145, 145, 145, 145, 139, 119, 76, 119, 27, 76, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 145, 145, 145, 145, 145, 145, 145, 139, 139, 119, 119, 119, 27, 27, 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: 788 number of broken/clashed sets: 112 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241245 none CNC(=O)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 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: [19, 19, 12, 19, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 6, 6, 12, 12, 32, 56, 145, 145, 145, 145, 145, 19, 19, 19, 19, 12, 12, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 32, 32, 145] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 353 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241245 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241245 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241245/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241245 Building REAL300025241246 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241246' /scratch/stefan/7787021/working/building/REAL300025241246 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241246 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241246/0 /scratch/stefan/7787021/working/building/REAL300025241246 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/103 `/scratch/stefan/7787021/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1COC1)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241246.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241246 none CC(OC1COC1)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 7, 3, 7, 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: [5, 3, 5, 10, 20, 20, 20, 1, 3, 1, 1, 1, 1, 1, 1, 3, 4, 4, 6, 6, 14, 25, 96, 96, 96, 96, 96, 5, 5, 5, 5, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 14, 14, 96] 201 rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 221 number of broken/clashed sets: 150 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241246 none CC(OC1COC1)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 7, 3, 7, 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: [159, 116, 159, 189, 201, 201, 201, 96, 116, 96, 96, 96, 96, 93, 68, 51, 68, 27, 51, 13, 1, 1, 1, 1, 1, 1, 1, 159, 159, 159, 159, 201, 201, 201, 201, 201, 96, 96, 96, 96, 96, 96, 96, 93, 93, 68, 68, 68, 27, 27, 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: 788 number of broken/clashed sets: 150 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241246 none CC(OC1COC1)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 7, 3, 7, 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: [11, 6, 1, 1, 1, 1, 1, 11, 20, 20, 20, 20, 20, 20, 20, 34, 37, 37, 44, 44, 85, 120, 201, 201, 201, 201, 201, 11, 11, 11, 11, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 34, 34, 37, 37, 37, 85, 85, 201] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 34, 35, 31] set([0, 1, 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: 602 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241246 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241246 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241246/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241246 Building REAL300025241247 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241247' /scratch/stefan/7787021/working/building/REAL300025241247 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241247 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241247/0 /scratch/stefan/7787021/working/building/REAL300025241247 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/104 `/scratch/stefan/7787021/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)C(F)F) `REAL300025241247.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241247 none CC(=CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 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 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 10] 10 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]) total number of confs: 22 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: REAL300025241247 none CC(=CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 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 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 5, 6, 8, 8, 8, 8, 8, 5, 6, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 8, 6] 10 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 30, 31] set([0, 1, 2, 4, 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]) total number of confs: 43 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241247 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241247 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241247/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241247 Building REAL300025241248 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241248' /scratch/stefan/7787021/working/building/REAL300025241248 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241248 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241248/0 /scratch/stefan/7787021/working/building/REAL300025241248 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/105 `/scratch/stefan/7787021/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C=CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241248.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241248 none CCOC(=O)C=CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 5, 7, 7, 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: [201, 200, 200, 132, 200, 132, 83, 81, 83, 81, 81, 81, 81, 68, 57, 41, 57, 17, 41, 10, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 132, 132, 81, 81, 81, 81, 81, 81, 81, 68, 68, 57, 57, 57, 17, 17, 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: 731 number of broken/clashed sets: 74 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241248 none CCOC(=O)C=CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 5, 7, 7, 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: [21, 13, 13, 6, 13, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 6, 6, 12, 12, 30, 40, 81, 81, 81, 81, 81, 21, 21, 21, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 30, 30, 81] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 274 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241248 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241248 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241248/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241248 Building REAL300025241249 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241249' /scratch/stefan/7787021/working/building/REAL300025241249 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241249 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241249/0 /scratch/stefan/7787021/working/building/REAL300025241249 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/106 `/scratch/stefan/7787021/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=NN=CN1C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241249.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241249 none CN(CC1CCCN1C(=O)C1=NN=CN1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 21, 12, 12, 12, 12, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 30, 65, 65, 101, 132, 201, 201, 201, 201, 201, 30, 30, 30, 21, 21, 12, 12, 12, 12, 12, 12, 12, 1, 2, 2, 2, 101, 101, 201] 201 rigid atoms, others: [38, 8, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 575 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: REAL300025241249 none CN(CC1CCCN1C(=O)C1=NN=CN1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 100, 120, 150, 151, 151, 151, 151, 151, 184, 184, 201, 201, 201, 201, 201, 41, 100, 13, 1, 1, 1, 1, 1, 1, 1, 120, 120, 120, 150, 150, 151, 151, 151, 151, 151, 151, 151, 201, 201, 201, 201, 41, 41, 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: 730 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: REAL300025241249 none CN(CC1CCCN1C(=O)C1=NN=CN1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 12, 12, 12, 12, 9, 18, 18, 34, 50, 151, 151, 151, 151, 151, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 34, 34, 151] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 315 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241249 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241249 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241249/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241249 Building REAL300025241250 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241250' /scratch/stefan/7787021/working/building/REAL300025241250 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241250 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241250/0 /scratch/stefan/7787021/working/building/REAL300025241250 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/107 `/scratch/stefan/7787021/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CN1C=NC(N)=N1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241250.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241250 none CN(CC1CCCN1C(=O)CN1C=NC(N)=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 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, 14, 7, 7, 7, 7, 7, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 16, 32, 32, 75, 111, 201, 201, 201, 201, 201, 16, 16, 16, 14, 14, 7, 7, 7, 7, 7, 7, 7, 5, 5, 1, 2, 2, 75, 75, 201] 201 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 552 number of broken/clashed sets: 73 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241250 none CN(CC1CCCN1C(=O)CN1C=NC(N)=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 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: [130, 86, 130, 158, 168, 168, 168, 168, 168, 168, 168, 201, 201, 201, 201, 201, 201, 29, 86, 13, 1, 1, 1, 1, 1, 1, 1, 130, 130, 130, 158, 158, 168, 168, 168, 168, 168, 168, 168, 201, 201, 201, 201, 201, 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: 800 number of broken/clashed sets: 73 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241250 none CN(CC1CCCN1C(=O)CN1C=NC(N)=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 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: [6, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 7, 7, 7, 7, 7, 6, 12, 12, 37, 62, 168, 168, 168, 168, 168, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 37, 37, 168] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 358 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241250 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241250 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241250/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241250 Building REAL300025241251 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241251' /scratch/stefan/7787021/working/building/REAL300025241251 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241251 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241251/0 /scratch/stefan/7787021/working/building/REAL300025241251 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/108 `/scratch/stefan/7787021/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CCCOCC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241251.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241251 none CN(CC1CCCN1C(=O)C1=CCCOCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 9, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 22, 47, 47, 85, 121, 201, 201, 201, 201, 201, 22, 22, 22, 18, 18, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 85, 85, 201] 201 rigid atoms, others: [45, 43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 554 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: REAL300025241251 none CN(CC1CCCN1C(=O)C1=CCCOCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 76, 77, 101, 103, 103, 103, 103, 103, 119, 119, 201, 201, 201, 201, 201, 201, 36, 76, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 101, 101, 103, 103, 103, 103, 103, 103, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 36, 36, 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: 631 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: REAL300025241251 none CN(CC1CCCN1C(=O)C1=CCCOCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 7, 13, 13, 28, 44, 103, 103, 103, 103, 103, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 28, 28, 103] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 245 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241251 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241251 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241251/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241251 Building REAL300025241252 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241252' /scratch/stefan/7787021/working/building/REAL300025241252 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241252 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241252/0 /scratch/stefan/7787021/working/building/REAL300025241252 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/109 `/scratch/stefan/7787021/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OCC[C@@H]1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241252.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241252 none C[C@@H]1OCC[C@@H]1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 12, 12, 35, 35, 76, 114, 195, 195, 195, 195, 195, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 76, 76, 195] 201 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 487 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241252 none C[C@@H]1OCC[C@@H]1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 7, 7, 7, 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: [201, 201, 201, 201, 201, 201, 201, 201, 195, 201, 195, 195, 195, 195, 193, 147, 114, 147, 39, 114, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 195, 195, 195, 195, 195, 195, 195, 193, 193, 147, 147, 147, 39, 39, 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: 758 number of broken/clashed sets: 60 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241252 none C[C@@H]1OCC[C@@H]1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 6, 18, 18, 41, 41, 86, 125, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 6, 6, 18, 18, 18, 86, 86, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 33, 31] set([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: 532 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241252 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241252 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241252/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241252 Building REAL300025241253 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241253' /scratch/stefan/7787021/working/building/REAL300025241253 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241253 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241253/0 /scratch/stefan/7787021/working/building/REAL300025241253 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/110 `/scratch/stefan/7787021/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1CC(F)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241253.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241253 none CN(CC1CCCN1C(=O)C1CC(F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7, 7] 0 hydrogens 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, 17, 10, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 22, 43, 43, 80, 116, 201, 201, 201, 201, 201, 22, 22, 22, 17, 17, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 80, 80, 201] 201 rigid atoms, others: [37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 530 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241253 none CN(CC1CCCN1C(=O)C1CC(F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7, 7] 0 hydrogens 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, 84, 91, 116, 119, 119, 119, 119, 119, 123, 123, 201, 201, 201, 201, 38, 84, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 116, 116, 119, 119, 119, 119, 119, 119, 119, 201, 201, 201, 201, 201, 201, 38, 38, 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: 787 number of broken/clashed sets: 58 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241253 none CN(CC1CCCN1C(=O)C1CC(F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 6, 12, 12, 29, 49, 119, 119, 119, 119, 119, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 29, 29, 119] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 283 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241253 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241253 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241253/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241253 Building REAL300025241254 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241254' /scratch/stefan/7787021/working/building/REAL300025241254 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241254 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241254/0 /scratch/stefan/7787021/working/building/REAL300025241254 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/111 `/scratch/stefan/7787021/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(O)C(C)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241254.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241254 none CCC(O)C(C)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 7, 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, 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, 170, 201, 114, 170, 114, 114, 114, 114, 114, 114, 109, 92, 70, 92, 27, 70, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 603, 170, 170, 170, 170, 114, 114, 114, 114, 114, 114, 114, 109, 109, 92, 92, 92, 27, 27, 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: 1535 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: REAL300025241254 none CCC(O)C(C)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 7, 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, 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: [6, 6, 4, 6, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 3, 4, 4, 11, 11, 31, 49, 114, 114, 114, 114, 114, 6, 6, 6, 6, 6, 6, 18, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 31, 31, 114] 603 rigid atoms, others: [43, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 294 number of broken/clashed sets: 189 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241254 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241254 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241254/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241254 Building REAL300025241255 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241255' /scratch/stefan/7787021/working/building/REAL300025241255 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241255 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241255/0 /scratch/stefan/7787021/working/building/REAL300025241255 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/112 `/scratch/stefan/7787021/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)OCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241255.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241255 none CCC(C)(C)OCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 145, 201, 201, 98, 33, 33, 33, 33, 33, 33, 33, 28, 25, 17, 25, 10, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 98, 98, 33, 33, 33, 33, 33, 33, 33, 28, 28, 25, 25, 25, 10, 10, 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: 788 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241255 none CCC(C)(C)OCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 64, 32, 64, 64, 15, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 6, 6, 9, 9, 11, 15, 33, 33, 33, 33, 33, 75, 75, 75, 75, 75, 64, 64, 64, 64, 64, 64, 15, 15, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 11, 11, 33] 201 rigid atoms, others: [45, 43, 7, 40, 9, 10, 11, 12, 13, 14, 44, 46, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 380 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241255 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241255 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241255/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241255 Building REAL300025241256 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241256' /scratch/stefan/7787021/working/building/REAL300025241256 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241256 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241256/0 /scratch/stefan/7787021/working/building/REAL300025241256 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/113 `/scratch/stefan/7787021/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC1CC(=O)N1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241256.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241256 none CN(CC1CCCN1C(=O)CC1CC(=O)N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 6, 6, 6, 6, 6, 6, 4, 6, 1, 1, 1, 1, 1, 1, 7, 9, 9, 12, 13, 17, 17, 17, 17, 17, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 12, 12, 17] 17 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46]) total number of confs: 56 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: REAL300025241256 none CN(CC1CCCN1C(=O)CC1CC(=O)N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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] 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: [14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 15, 17, 17, 17, 17, 14, 14, 9, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 15, 15, 17, 17, 17, 17, 14, 14, 1] 17 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: 54 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: REAL300025241256 none CN(CC1CCCN1C(=O)CC1CC(=O)N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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] 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: [3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 6, 6, 6, 6, 3, 4, 4, 7, 9, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 7, 7, 14] 17 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 58 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241256 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241256 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241256/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241256 Building REAL300025241257 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241257' /scratch/stefan/7787021/working/building/REAL300025241257 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241257 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241257/0 /scratch/stefan/7787021/working/building/REAL300025241257 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/114 `/scratch/stefan/7787021/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C(O)C1CCC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241257.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241257 none CN(CC1CCCN1C(=O)C(O)C1CCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 5, 5, 5, 5, 5, 4, 2, 4, 1, 2, 1, 1, 1, 1, 6, 7, 7, 10, 11, 13, 13, 13, 13, 13, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 2, 6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 13] 39 rigid atoms, others: [45, 40, 41, 10, 43, 12, 13, 14, 15, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49]) total number of confs: 52 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: REAL300025241257 none CN(CC1CCCN1C(=O)C(O)C1CCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 13, 13, 13, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 13, 39, 13, 13, 13, 13, 13, 13, 13, 11, 11, 1] 39 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: 78 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: REAL300025241257 none CN(CC1CCCN1C(=O)C(O)C1CCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 3, 4, 4, 7, 9, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 15, 5, 5, 5, 5, 5, 5, 5, 7, 7, 11] 39 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 64 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241257 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241257 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241257/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241257 Building REAL300025241258 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241258' /scratch/stefan/7787021/working/building/REAL300025241258 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241258 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241258/0 /scratch/stefan/7787021/working/building/REAL300025241258 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/115 `/scratch/stefan/7787021/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1CCOC(=O)N1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241258.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241258 none CN(CC1CCCN1C(=O)C1CCOC(=O)N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 6, 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] 0 hydrogens 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, 10, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 27, 50, 50, 92, 127, 201, 201, 201, 201, 201, 27, 27, 27, 19, 19, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 92, 92, 201] 201 rigid atoms, others: [43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 552 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241258 none CN(CC1CCCN1C(=O)C1CCOC(=O)N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 6, 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] 0 hydrogens 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, 104, 123, 160, 166, 166, 166, 166, 166, 169, 169, 201, 201, 201, 201, 201, 201, 41, 104, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 160, 160, 166, 166, 166, 166, 166, 166, 166, 201, 201, 201, 201, 201, 201, 41, 41, 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: 770 number of broken/clashed sets: 64 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241258 none CN(CC1CCCN1C(=O)C1CCOC(=O)N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 6, 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] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 10, 10, 22, 22, 54, 87, 166, 166, 166, 166, 166, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 54, 54, 166] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 410 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241258 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241258 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241258/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241258 Building REAL300025241259 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241259' /scratch/stefan/7787021/working/building/REAL300025241259 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241259 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241259/0 /scratch/stefan/7787021/working/building/REAL300025241259 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/116 `/scratch/stefan/7787021/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC1C[NH+](C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241259.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241259 none CN(CC1CCCN1C(=O)CC1C[NH+](C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 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: [10, 10, 10, 10, 10, 10, 10, 9, 5, 9, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 20, 20, 24, 24, 24, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 1, 1, 1, 2, 2, 2, 1, 1, 20, 20, 24] 24 rigid atoms, others: [48, 43, 41, 10, 11, 12, 13, 14, 15, 16, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 49, 50, 51]) total number of confs: 91 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: REAL300025241259 none CN(CC1CCCN1C(=O)CC1C[NH+](C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 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: [19, 18, 19, 19, 19, 19, 19, 19, 19, 19, 19, 23, 24, 24, 24, 24, 24, 15, 18, 13, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 15, 15, 1] 24 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: 67 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: REAL300025241259 none CN(CC1CCCN1C(=O)CC1C[NH+](C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 10, 10, 10, 10, 10, 3, 3, 3, 9, 10, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 19] 24 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 80 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241259 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241259 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241259/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241259 Building REAL300025241260 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241260' /scratch/stefan/7787021/working/building/REAL300025241260 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241260 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241260/0 /scratch/stefan/7787021/working/building/REAL300025241260 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/117 `/scratch/stefan/7787021/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)S1) `REAL300025241260.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241260 none CC1=NN=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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: [6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 8, 8, 17, 17, 44, 75, 159, 159, 159, 159, 159, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 44, 44, 159] 201 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 363 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: REAL300025241260 none CC1=NN=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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: [201, 201, 201, 201, 201, 159, 201, 159, 159, 159, 159, 155, 116, 77, 116, 29, 77, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 159, 159, 159, 159, 159, 159, 159, 155, 155, 116, 116, 116, 29, 29, 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: 773 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: REAL300025241260 none CC1=NN=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 1, 1, 4, 4, 6, 6, 6, 6, 6, 12, 18, 18, 39, 39, 86, 119, 201, 201, 201, 201, 201, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 12, 12, 18, 18, 18, 86, 86, 201] 201 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: 541 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241260 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241260 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241260/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241260 Building REAL300025241261 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241261' /scratch/stefan/7787021/working/building/REAL300025241261 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241261 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241261/0 /scratch/stefan/7787021/working/building/REAL300025241261 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/118 `/scratch/stefan/7787021/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1CC(C)(O)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241261.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241261 none CN(CC1CCCN1C(=O)C1CC(C)(O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 17, 9, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 23, 46, 46, 85, 119, 201, 201, 201, 201, 201, 23, 23, 23, 17, 17, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 2, 2, 2, 6, 1, 1, 85, 85, 201] 603 rigid atoms, others: [45, 38, 39, 8, 10, 11, 12, 13, 14, 15, 40, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 562 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241261 none CN(CC1CCCN1C(=O)C1CC(C)(O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [97, 89, 97, 122, 129, 129, 129, 129, 129, 134, 134, 201, 201, 201, 201, 201, 38, 89, 13, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 122, 122, 129, 129, 129, 129, 129, 129, 129, 201, 201, 201, 201, 201, 201, 603, 201, 201, 38, 38, 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: 1386 number of broken/clashed sets: 174 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241261 none CN(CC1CCCN1C(=O)C1CC(C)(O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [6, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 9, 6, 12, 12, 32, 53, 129, 129, 129, 129, 129, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 27, 9, 9, 32, 32, 129] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 325 number of broken/clashed sets: 174 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241261 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241261 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241261/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241261 Building REAL300025241262 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241262' /scratch/stefan/7787021/working/building/REAL300025241262 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241262 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241262/0 /scratch/stefan/7787021/working/building/REAL300025241262 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/119 `/scratch/stefan/7787021/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241262.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241262 none CCCCCC(O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 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, 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: [199, 199, 170, 150, 84, 30, 84, 30, 30, 30, 30, 30, 30, 26, 26, 16, 26, 9, 16, 7, 1, 1, 1, 1, 1, 1, 1, 200, 201, 201, 201, 200, 201, 201, 170, 170, 151, 151, 84, 252, 30, 30, 30, 30, 30, 30, 30, 26, 26, 26, 26, 26, 9, 9, 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: 1209 number of broken/clashed sets: 219 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241262 none CCCCCC(O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 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, 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: [63, 50, 37, 30, 8, 3, 8, 1, 3, 1, 1, 1, 1, 1, 1, 4, 5, 5, 7, 7, 11, 15, 30, 30, 30, 30, 30, 64, 65, 65, 65, 64, 52, 52, 37, 36, 31, 31, 8, 24, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 11, 11, 30] 603 rigid atoms, others: [45, 43, 7, 40, 9, 10, 11, 12, 13, 14, 44, 46, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 409 number of broken/clashed sets: 219 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241262 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241262 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241262/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241262 Building REAL300025241263 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241263' /scratch/stefan/7787021/working/building/REAL300025241263 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241263 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241263/0 /scratch/stefan/7787021/working/building/REAL300025241263 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/120 `/scratch/stefan/7787021/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CC=CC(N)=N1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241263.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241263 none CN(CC1CCCN1C(=O)C1=CC=CC(N)=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 3, 7, 6, 7, 7, 7, 7, 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: [21, 18, 10, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 21, 48, 48, 84, 118, 201, 201, 201, 201, 201, 21, 21, 21, 18, 18, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 2, 2, 84, 84, 201] 201 rigid atoms, others: [39, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46]) total number of confs: 546 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: REAL300025241263 none CN(CC1CCCN1C(=O)C1=CC=CC(N)=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 3, 7, 6, 7, 7, 7, 7, 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: [107, 95, 107, 138, 139, 139, 139, 139, 139, 182, 182, 201, 201, 201, 201, 201, 201, 39, 95, 13, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 138, 138, 139, 139, 139, 139, 139, 139, 139, 201, 201, 201, 201, 201, 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: 720 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: REAL300025241263 none CN(CC1CCCN1C(=O)C1=CC=CC(N)=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 3, 7, 6, 7, 7, 7, 7, 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, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 10, 10, 7, 12, 12, 27, 48, 139, 139, 139, 139, 139, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 27, 27, 139] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 290 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241263 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241263 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241263/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241263 Building REAL300025241264 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241264' /scratch/stefan/7787021/working/building/REAL300025241264 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241264 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241264/0 /scratch/stefan/7787021/working/building/REAL300025241264 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/121 `/scratch/stefan/7787021/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CC=C(O)C=C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241264.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241264 none CN(CC1CCCN1C(=O)C1=CC=C(O)C=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [19, 13, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 19, 47, 47, 91, 120, 201, 201, 201, 201, 201, 19, 19, 19, 13, 13, 6, 6, 6, 6, 6, 6, 6, 1, 1, 2, 1, 1, 91, 91, 201] 402 rigid atoms, others: [43, 39, 8, 10, 11, 12, 13, 14, 15, 16, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 44, 45, 46]) total number of confs: 551 number of broken/clashed sets: 194 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241264 none CN(CC1CCCN1C(=O)C1=CC=C(O)C=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [132, 86, 132, 163, 182, 182, 182, 182, 182, 201, 201, 201, 201, 201, 201, 201, 201, 28, 86, 13, 1, 1, 1, 1, 1, 1, 1, 132, 132, 132, 163, 163, 182, 182, 182, 182, 182, 182, 182, 201, 201, 402, 201, 201, 28, 28, 1] 402 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: 1135 number of broken/clashed sets: 194 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241264 none CN(CC1CCCN1C(=O)C1=CC=C(O)C=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 5, 5, 6, 6, 7, 19, 19, 50, 79, 182, 182, 182, 182, 182, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 6, 6, 50, 50, 182] 402 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 425 number of broken/clashed sets: 194 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241264 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241264 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241264/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241264 Building REAL300025241265 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241265' /scratch/stefan/7787021/working/building/REAL300025241265 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241265 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241265/0 /scratch/stefan/7787021/working/building/REAL300025241265 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/122 `/scratch/stefan/7787021/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241265.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241265 none C=CCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1] 22 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]) total number of confs: 84 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: REAL300025241265 none C=CCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 6, 8, 11, 11, 11, 11, 11, 10, 10, 10, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 11] 22 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 66 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241265 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241265 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241265/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241265 Building REAL300025241266 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241266' /scratch/stefan/7787021/working/building/REAL300025241266 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241266 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241266/0 /scratch/stefan/7787021/working/building/REAL300025241266 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/123 `/scratch/stefan/7787021/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C[NH+](C)C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241266.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241266 none CN(CC1CCCN1C(=O)C[NH+](C)C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 16, 16, 16, 16, 16, 16, 17, 17, 18, 18, 18, 18, 12, 15, 9, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 16, 16, 16, 16, 16, 16, 16, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 12, 12, 1] 18 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: 56 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: REAL300025241266 none CN(CC1CCCN1C(=O)C[NH+](C)C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 3, 4, 4, 8, 11, 16, 16, 16, 16, 16, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 16] 18 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 73 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241266 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241266/1 /scratch/stefan/7787021/working/building/REAL300025241266 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/124 `/scratch/stefan/7787021/working/3D/124' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241266.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241266/1/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: REAL300025241266 none CN(C)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1] 12 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: 28 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: REAL300025241266 none CN(C)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 6, 8, 11, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 11] 12 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]) total number of confs: 47 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241266 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241266 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241266/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241266/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241266 Building REAL300025241267 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241267' /scratch/stefan/7787021/working/building/REAL300025241267 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241267 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241267/0 /scratch/stefan/7787021/working/building/REAL300025241267 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/125 `/scratch/stefan/7787021/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CC=CC(N)=C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241267.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241267 none CN(CC1CCCN1C(=O)C1=CC=CC(N)=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 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, 22, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 26, 58, 58, 101, 128, 201, 201, 201, 201, 201, 26, 26, 26, 22, 22, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 2, 2, 1, 101, 101, 201] 201 rigid atoms, others: [39, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 45, 46, 47]) total number of confs: 595 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241267 none CN(CC1CCCN1C(=O)C1=CC=CC(N)=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 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: [66, 66, 66, 87, 90, 90, 90, 90, 90, 110, 110, 201, 201, 201, 201, 201, 201, 34, 66, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 87, 87, 90, 90, 90, 90, 90, 90, 90, 201, 201, 201, 201, 201, 201, 34, 34, 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: 600 number of broken/clashed sets: 63 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241267 none CN(CC1CCCN1C(=O)C1=CC=CC(N)=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 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: [7, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 11, 7, 13, 13, 27, 39, 90, 90, 90, 90, 90, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 27, 27, 90] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 221 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241267 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241267 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241267/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241267 Building REAL300025241268 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241268' /scratch/stefan/7787021/working/building/REAL300025241268 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241268 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241268/0 /scratch/stefan/7787021/working/building/REAL300025241268 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/126 `/scratch/stefan/7787021/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC#N)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241268.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241268 none CN(CC1CCCN1C(=O)CC#N)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 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: [111, 104, 111, 153, 155, 155, 155, 155, 155, 156, 156, 201, 201, 42, 104, 13, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 153, 153, 155, 155, 155, 155, 155, 155, 155, 201, 201, 42, 42, 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: 858 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: REAL300025241268 none CN(CC1CCCN1C(=O)CC#N)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 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, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 18, 9, 18, 18, 37, 61, 155, 155, 155, 155, 155, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 18, 18, 37, 37, 155] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39]) total number of confs: 380 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241268 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241268 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241268/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241268 Building REAL300025241269 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241269' /scratch/stefan/7787021/working/building/REAL300025241269 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241269 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241269/0 /scratch/stefan/7787021/working/building/REAL300025241269 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/127 `/scratch/stefan/7787021/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CC=C(N)C=C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241269.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241269 none CN(CC1CCCN1C(=O)C1=CC=C(N)C=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [18, 13, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 18, 42, 42, 82, 112, 201, 201, 201, 201, 201, 18, 18, 18, 13, 13, 6, 6, 6, 6, 6, 6, 6, 1, 1, 2, 2, 1, 1, 82, 82, 201] 201 rigid atoms, others: [43, 39, 8, 44, 10, 11, 12, 13, 14, 15, 16, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 45, 46, 47]) total number of confs: 539 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: REAL300025241269 none CN(CC1CCCN1C(=O)C1=CC=C(N)C=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [140, 98, 140, 165, 177, 177, 177, 177, 177, 201, 201, 201, 201, 201, 201, 201, 201, 30, 98, 13, 1, 1, 1, 1, 1, 1, 1, 140, 140, 140, 165, 165, 177, 177, 177, 177, 177, 177, 177, 201, 201, 201, 201, 201, 201, 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: 706 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: REAL300025241269 none CN(CC1CCCN1C(=O)C1=CC=C(N)C=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [6, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 18, 18, 50, 79, 177, 177, 177, 177, 177, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 50, 50, 177] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 403 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241269 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241269 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241269/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241269 Building REAL300025241270 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241270' /scratch/stefan/7787021/working/building/REAL300025241270 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241270 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241270/0 /scratch/stefan/7787021/working/building/REAL300025241270 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/128 `/scratch/stefan/7787021/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CC=CN=C1F)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241270.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241270 none CN(CC1CCCN1C(=O)C1=CC=CN=C1F)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 15, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 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, 24, 13, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 32, 63, 63, 103, 136, 201, 201, 201, 201, 201, 32, 32, 32, 24, 24, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 103, 103, 201] 201 rigid atoms, others: [39, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44]) total number of confs: 601 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: REAL300025241270 none CN(CC1CCCN1C(=O)C1=CC=CN=C1F)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 15, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 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: [92, 86, 92, 126, 131, 131, 131, 131, 131, 152, 152, 201, 201, 201, 201, 201, 201, 37, 86, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 126, 126, 131, 131, 131, 131, 131, 131, 131, 201, 201, 201, 37, 37, 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: 678 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: REAL300025241270 none CN(CC1CCCN1C(=O)C1=CC=CN=C1F)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 15, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 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, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 13, 13, 13, 9, 19, 19, 39, 63, 131, 131, 131, 131, 131, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 39, 39, 131] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44]) total number of confs: 316 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241270 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241270 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241270/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241270 Building REAL300025241271 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241271' /scratch/stefan/7787021/working/building/REAL300025241271 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241271 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241271/0 /scratch/stefan/7787021/working/building/REAL300025241271 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/129 `/scratch/stefan/7787021/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1C(C)C1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241271.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241271 none CCOC1C(C)C1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 6, 6, 14, 14, 36, 57, 192, 192, 192, 192, 192, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 36, 36, 192] 201 rigid atoms, others: [43, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 370 number of broken/clashed sets: 68 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241271 none CCOC1C(C)C1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 192, 192, 192, 192, 192, 192, 192, 192, 177, 139, 91, 139, 30, 91, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 192, 192, 192, 192, 192, 192, 192, 192, 192, 192, 192, 192, 192, 177, 177, 139, 139, 139, 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: 732 number of broken/clashed sets: 68 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241271 none CCOC1C(C)C1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 6, 6, 14, 14, 36, 57, 192, 192, 192, 192, 192, 4, 4, 4, 4, 4, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 4, 4, 6, 6, 6, 36, 36, 192] 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: 374 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241271 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241271 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241271/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241271 Building REAL300025241272 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241272' /scratch/stefan/7787021/working/building/REAL300025241272 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241272 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241272/0 /scratch/stefan/7787021/working/building/REAL300025241272 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/130 `/scratch/stefan/7787021/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1CC1F)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241272.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241272 none CN(CC1CCCN1C(=O)C1CC1F)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 1, 27, 49, 49, 85, 121, 201, 201, 201, 201, 201, 27, 27, 27, 19, 19, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 85, 85, 201] 201 rigid atoms, others: [36, 37, 38, 39, 8, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 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]) total number of confs: 552 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241272 none CN(CC1CCCN1C(=O)C1CC1F)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 83, 89, 118, 119, 119, 119, 119, 119, 128, 128, 201, 201, 201, 38, 83, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 118, 118, 119, 119, 119, 119, 119, 119, 119, 201, 201, 201, 201, 38, 38, 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: 791 number of broken/clashed sets: 53 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241272 none CN(CC1CCCN1C(=O)C1CC1F)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 12, 12, 9, 16, 16, 34, 53, 119, 119, 119, 119, 119, 9, 9, 9, 3, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 34, 34, 119] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 293 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241272 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241272 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241272/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241272 Building REAL300025241273 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241273' /scratch/stefan/7787021/working/building/REAL300025241273 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241273 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241273/0 /scratch/stefan/7787021/working/building/REAL300025241273 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/131 `/scratch/stefan/7787021/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)COC1(C)CCC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241273.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241273 none CN(CC1CCCN1C(=O)COC1(C)CCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [28, 26, 14, 14, 14, 14, 14, 14, 9, 14, 5, 1, 1, 1, 1, 1, 1, 28, 34, 34, 77, 115, 201, 201, 201, 201, 201, 28, 28, 28, 26, 26, 14, 14, 14, 14, 14, 14, 14, 9, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 77, 77, 201] 201 rigid atoms, others: [48, 45, 44, 11, 12, 13, 14, 15, 16, 49, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 580 number of broken/clashed sets: 144 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241273 none CN(CC1CCCN1C(=O)COC1(C)CCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 59, 72, 99, 101, 101, 101, 101, 101, 101, 101, 141, 199, 201, 201, 201, 201, 28, 59, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 99, 99, 101, 101, 101, 101, 101, 101, 101, 141, 141, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 770 number of broken/clashed sets: 144 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241273 none CN(CC1CCCN1C(=O)COC1(C)CCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [4, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 14, 14, 14, 14, 4, 6, 6, 14, 24, 101, 101, 101, 101, 101, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 101] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 215 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241273 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241273 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241273/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241273 Building REAL300025241274 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241274' /scratch/stefan/7787021/working/building/REAL300025241274 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241274 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241274/0 /scratch/stefan/7787021/working/building/REAL300025241274 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/132 `/scratch/stefan/7787021/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)[NH+](C)C) `REAL300025241274.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241274 none C[C@@H](C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)[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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 15, 14, 14, 8, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 14, 1, 15, 15, 15, 15, 15, 15] 15 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: 43 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: REAL300025241274 none C[C@@H](C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)[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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 5, 1, 4, 1, 1, 1, 1, 1, 1, 4, 5, 5, 8, 8, 11, 12, 15, 15, 15, 15, 15, 5, 7, 7, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 11, 11, 15, 7, 7, 7, 7, 7, 7] 15 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 30, 31] set([0, 1, 2, 4, 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]) total number of confs: 75 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241274 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241274/1 /scratch/stefan/7787021/working/building/REAL300025241274 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/133 `/scratch/stefan/7787021/working/3D/133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)N(C)C) `REAL300025241274.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241274/1/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: REAL300025241274 none C[C@@H](C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 13, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 13, 13, 13, 13, 13, 13] 13 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: 39 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: REAL300025241274 none C[C@@H](C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 7, 8, 11, 11, 11, 11, 11, 6, 7, 7, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 11, 7, 7, 7, 7, 7, 7] 13 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 35, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241274 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241274 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241274/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241274/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241274 Building REAL300025241275 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241275' /scratch/stefan/7787021/working/building/REAL300025241275 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241275 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241275/0 /scratch/stefan/7787021/working/building/REAL300025241275 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/134 `/scratch/stefan/7787021/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CN=C(N)N=C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241275.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241275 none CN(CC1CCCN1C(=O)C1=CN=C(N)N=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 8, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 3, 7, 7, 6, 7, 7, 7, 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, 12, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 16, 37, 37, 81, 112, 201, 201, 201, 201, 201, 16, 16, 16, 12, 12, 6, 6, 6, 6, 6, 6, 6, 1, 2, 2, 1, 81, 81, 201] 201 rigid atoms, others: [39, 8, 10, 11, 12, 13, 14, 15, 16, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 43, 44, 45]) total number of confs: 533 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241275 none CN(CC1CCCN1C(=O)C1=CN=C(N)N=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 8, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 3, 7, 7, 6, 7, 7, 7, 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: [145, 94, 145, 168, 180, 180, 180, 180, 180, 201, 201, 201, 201, 201, 201, 201, 201, 31, 94, 13, 1, 1, 1, 1, 1, 1, 1, 145, 145, 145, 168, 168, 180, 180, 180, 180, 180, 180, 180, 201, 201, 201, 201, 31, 31, 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: 710 number of broken/clashed sets: 84 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241275 none CN(CC1CCCN1C(=O)C1=CN=C(N)N=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 8, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 3, 7, 7, 6, 7, 7, 7, 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, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 4, 4, 6, 6, 7, 19, 19, 49, 77, 180, 180, 180, 180, 180, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 49, 49, 180] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 410 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241275 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241275 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241275/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241275 Building REAL300025241276 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241276' /scratch/stefan/7787021/working/building/REAL300025241276 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241276 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241276/0 /scratch/stefan/7787021/working/building/REAL300025241276 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/135 `/scratch/stefan/7787021/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CCF)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241276.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241276 none CN(CC1CCCN1C(=O)CCF)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 15, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 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 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 10, 10, 8, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 10, 10, 1] 12 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: 30 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: REAL300025241276 none CN(CC1CCCN1C(=O)CCF)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 15, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 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 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 2, 3, 3, 6, 8, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 6, 10] 12 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 46 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241276 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241276 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241276/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241276 Building REAL300025241277 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241277' /scratch/stefan/7787021/working/building/REAL300025241277 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241277 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241277/0 /scratch/stefan/7787021/working/building/REAL300025241277 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/136 `/scratch/stefan/7787021/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CC(F)=NN1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241277.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241277 none CN(CC1CCCN1C(=O)C1=CC(F)=NN1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'N.2', 'N.pl3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 15, 8, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 22, 13, 13, 13, 13, 13, 9, 1, 9, 1, 1, 1, 1, 1, 1, 32, 60, 60, 87, 123, 201, 201, 201, 201, 201, 32, 32, 32, 22, 22, 13, 13, 13, 13, 13, 13, 13, 1, 1, 87, 87, 201] 201 rigid atoms, others: [38, 39, 8, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 541 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: REAL300025241277 none CN(CC1CCCN1C(=O)C1=CC(F)=NN1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'N.2', 'N.pl3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 15, 8, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 80, 88, 109, 116, 116, 116, 116, 116, 158, 158, 201, 201, 201, 201, 201, 39, 80, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 109, 109, 116, 116, 116, 116, 116, 116, 116, 201, 201, 39, 39, 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: 690 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: REAL300025241277 none CN(CC1CCCN1C(=O)C1=CC(F)=NN1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'N.2', 'N.pl3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 15, 8, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 4, 4, 13, 13, 13, 13, 13, 8, 14, 14, 25, 42, 116, 116, 116, 116, 116, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 13, 13, 25, 25, 116] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42]) total number of confs: 250 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241277 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241277 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241277/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241277 Building REAL300025241278 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241278' /scratch/stefan/7787021/working/building/REAL300025241278 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241278 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241278/0 /scratch/stefan/7787021/working/building/REAL300025241278 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/137 `/scratch/stefan/7787021/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1C=CCC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241278.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241278 none CN(CC1CCCN1C(=O)C1C=CCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 24, 41, 41, 83, 123, 201, 201, 201, 201, 201, 24, 24, 24, 16, 16, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 83, 83, 201] 201 rigid atoms, others: [43, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46]) total number of confs: 532 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: REAL300025241278 none CN(CC1CCCN1C(=O)C1C=CCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 95, 113, 147, 154, 154, 154, 154, 154, 156, 156, 201, 201, 201, 201, 39, 95, 13, 1, 1, 1, 1, 1, 1, 1, 113, 113, 113, 147, 147, 154, 154, 154, 154, 154, 154, 154, 201, 201, 201, 201, 201, 201, 201, 39, 39, 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: 785 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: REAL300025241278 none CN(CC1CCCN1C(=O)C1C=CCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 4, 9, 9, 9, 9, 9, 19, 19, 43, 69, 154, 154, 154, 154, 154, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 43, 43, 154] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 357 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241278 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241278 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241278/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241278 Building REAL300025241279 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241279' /scratch/stefan/7787021/working/building/REAL300025241279 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241279 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241279/0 /scratch/stefan/7787021/working/building/REAL300025241279 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/138 `/scratch/stefan/7787021/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1CCCC(O)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241279.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241279 none CN(CC1CCCN1C(=O)C1CCCC(O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 15, 9, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 25, 54, 54, 91, 122, 201, 201, 201, 201, 201, 25, 25, 25, 15, 15, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 91, 91, 201] 603 rigid atoms, others: [48, 45, 43, 49, 39, 8, 41, 10, 11, 12, 13, 14, 44, 16, 40, 46, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 50, 51, 52]) total number of confs: 532 number of broken/clashed sets: 177 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241279 none CN(CC1CCCN1C(=O)C1CCCC(O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [109, 96, 109, 136, 144, 144, 144, 144, 144, 153, 153, 201, 201, 201, 201, 201, 201, 37, 96, 13, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 136, 136, 144, 144, 144, 144, 144, 144, 144, 201, 201, 201, 201, 201, 201, 201, 201, 603, 201, 201, 37, 37, 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: 1369 number of broken/clashed sets: 177 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241279 none CN(CC1CCCN1C(=O)C1CCCC(O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 9, 9, 10, 26, 26, 50, 73, 144, 144, 144, 144, 144, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 27, 9, 9, 50, 50, 144] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 382 number of broken/clashed sets: 177 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241279 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241279 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241279/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241279 Building REAL300025241280 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241280' /scratch/stefan/7787021/working/building/REAL300025241280 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241280 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241280/0 /scratch/stefan/7787021/working/building/REAL300025241280 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/139 `/scratch/stefan/7787021/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C=CC1CCOC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241280.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241280 none CN(CC1CCCN1C(=O)C=CC1CCOC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 14, 4, 14, 4, 1, 1, 1, 1, 1, 1, 27, 35, 35, 74, 116, 201, 201, 201, 201, 201, 27, 27, 27, 25, 25, 14, 14, 14, 14, 14, 14, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 74, 74, 201] 201 rigid atoms, others: [45, 43, 41, 42, 11, 12, 13, 14, 15, 16, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50]) total number of confs: 552 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241280 none CN(CC1CCCN1C(=O)C=CC1CCOC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 74, 103, 125, 126, 126, 126, 126, 126, 126, 126, 198, 198, 201, 201, 201, 201, 28, 74, 13, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 125, 125, 126, 126, 126, 126, 126, 126, 126, 198, 198, 201, 201, 201, 201, 201, 201, 201, 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: 685 number of broken/clashed sets: 124 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241280 none CN(CC1CCCN1C(=O)C=CC1CCOC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 2, 2, 9, 9, 14, 14, 14, 14, 4, 7, 7, 22, 40, 126, 126, 126, 126, 126, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 14, 14, 14, 14, 14, 14, 14, 22, 22, 126] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 271 number of broken/clashed sets: 124 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241280 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241280 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241280/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241280 Building REAL300025241281 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241281' /scratch/stefan/7787021/working/building/REAL300025241281 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241281 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241281/0 /scratch/stefan/7787021/working/building/REAL300025241281 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/140 `/scratch/stefan/7787021/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241281.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241281 none COC(C)C(O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 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] 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, 151, 146, 201, 141, 146, 141, 141, 141, 141, 132, 111, 70, 111, 27, 70, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 603, 141, 141, 141, 141, 141, 141, 141, 132, 132, 111, 111, 111, 27, 27, 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: 1792 number of broken/clashed sets: 277 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241281 none COC(C)C(O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 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] 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, 6, 6, 3, 6, 1, 3, 1, 1, 1, 1, 1, 1, 4, 6, 6, 14, 14, 42, 64, 141, 141, 141, 141, 141, 7, 7, 7, 7, 7, 7, 7, 6, 18, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 42, 42, 141] 603 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 365 number of broken/clashed sets: 277 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241281 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241281 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241281/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241281 Building REAL300025241282 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241282' /scratch/stefan/7787021/working/building/REAL300025241282 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241282 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241282/0 /scratch/stefan/7787021/working/building/REAL300025241282 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/141 `/scratch/stefan/7787021/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)[C@H]1CNC(=O)N1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241282.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241282 none CN(CC1CCCN1C(=O)[C@H]1CNC(=O)N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 22, 11, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 30, 49, 49, 84, 120, 201, 201, 201, 201, 201, 30, 30, 30, 22, 22, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 84, 84, 201] 201 rigid atoms, others: [39, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 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]) total number of confs: 551 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241282 none CN(CC1CCCN1C(=O)[C@H]1CNC(=O)N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 99, 101, 142, 152, 152, 152, 152, 152, 156, 156, 201, 201, 201, 201, 201, 201, 42, 99, 12, 1, 1, 1, 1, 1, 1, 1, 101, 101, 101, 142, 142, 152, 152, 152, 152, 152, 152, 152, 201, 201, 201, 201, 42, 42, 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: 795 number of broken/clashed sets: 61 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241282 none CN(CC1CCCN1C(=O)[C@H]1CNC(=O)N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 11, 10, 19, 19, 41, 68, 152, 152, 152, 152, 152, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 41, 41, 152] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 360 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241282 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241282 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241282/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241282 Building REAL300025241283 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241283' /scratch/stefan/7787021/working/building/REAL300025241283 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241283 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241283/0 /scratch/stefan/7787021/working/building/REAL300025241283 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/142 `/scratch/stefan/7787021/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSC(C)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241283.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241283 none CCSC(C)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 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: [201, 201, 191, 173, 191, 172, 173, 172, 172, 172, 172, 166, 132, 88, 132, 29, 88, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 191, 191, 191, 191, 172, 172, 172, 172, 172, 172, 172, 166, 166, 132, 132, 132, 29, 29, 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: 767 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: REAL300025241283 none CCSC(C)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 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: [10, 9, 6, 3, 6, 1, 3, 1, 1, 1, 1, 1, 1, 4, 7, 7, 14, 14, 41, 69, 172, 172, 172, 172, 172, 10, 10, 10, 10, 10, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 41, 41, 172] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 381 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241283 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241283 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241283/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241283 Building REAL300025241284 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241284' /scratch/stefan/7787021/working/building/REAL300025241284 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241284 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241284/0 /scratch/stefan/7787021/working/building/REAL300025241284 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/143 `/scratch/stefan/7787021/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)[NH+]1CC(C)C1) `REAL300025241284.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241284 none CC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)[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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 22, 23, 22, 22, 22, 22, 21, 21, 19, 21, 11, 19, 9, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 22, 22, 22, 22, 22, 22, 22, 21, 21, 21, 21, 21, 11, 11, 1, 23, 23, 23, 23, 23, 23, 23, 23] 23 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]) total number of confs: 64 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: REAL300025241284 none CC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)[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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 4, 4, 4, 4, 4, 4, 4, 6, 7, 7, 10, 10, 16, 16, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 6, 6, 7, 7, 7, 16, 16, 23, 1, 1, 1, 2, 2, 2, 1, 1] 23 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: 88 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: REAL300025241284 none CC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)[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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 5, 5, 8, 8, 14, 15, 22, 22, 22, 22, 22, 3, 4, 4, 4, 4, 4, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 14, 14, 22, 4, 4, 4, 4, 4, 4, 4, 4] 23 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37] set([0, 1, 3, 10, 11, 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, 51, 52, 53, 54]) total number of confs: 84 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241284 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241284/1 /scratch/stefan/7787021/working/building/REAL300025241284 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/144 `/scratch/stefan/7787021/working/3D/144' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)N1CC(C)C1) `REAL300025241284.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241284/1/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: REAL300025241284 none CC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 187, 200, 187, 187, 187, 187, 176, 145, 98, 145, 30, 97, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 187, 187, 187, 187, 187, 187, 187, 176, 176, 145, 145, 145, 30, 30, 1, 201, 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]) total number of confs: 738 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: REAL300025241284 none CC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 7, 7, 7, 7, 7, 15, 19, 19, 38, 38, 86, 115, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 15, 15, 19, 19, 19, 86, 86, 201, 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: 565 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: REAL300025241284 none CC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 6, 6, 14, 14, 41, 62, 187, 187, 187, 187, 187, 5, 7, 7, 7, 7, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 41, 41, 187, 7, 7, 7, 7, 7, 7, 7, 7] 201 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 37, 31] set([0, 1, 3, 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]) total number of confs: 388 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241284 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241284 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241284/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241284/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241284 Building REAL300025241285 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241285' /scratch/stefan/7787021/working/building/REAL300025241285 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300025241285 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241285/0 /scratch/stefan/7787021/working/building/REAL300025241285 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/145 `/scratch/stefan/7787021/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN1CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241285.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241285 none CC1CCN1CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 5, 5, 14, 14, 40, 66, 154, 154, 154, 154, 154, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 40, 40, 154] 201 rigid atoms, others: [36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 346 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241285 none CC1CCN1CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need 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, 154, 154, 154, 154, 154, 154, 154, 143, 119, 80, 119, 28, 80, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 154, 154, 154, 154, 154, 154, 154, 143, 143, 119, 119, 119, 28, 28, 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: 841 number of broken/clashed sets: 78 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241285 none CC1CCN1CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations 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, 4, 5, 5, 5, 5, 5, 5, 5, 11, 14, 14, 32, 32, 77, 111, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 11, 11, 14, 14, 14, 77, 77, 201] 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: 542 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241285 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241285/1 /scratch/stefan/7787021/working/building/REAL300025241285 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/146 `/scratch/stefan/7787021/working/3D/146' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC[N@@H+]1CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241285.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241285/1/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: REAL300025241285 none CC1CC[N@@H+]1CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 7, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 15, 24, 50, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 10, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 50] 50 rigid atoms, others: [43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 147 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: REAL300025241285 none CC1CC[N@@H+]1CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations 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, 48, 50, 27, 48, 12, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 1] 50 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: 163 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: REAL300025241285 none CC1CC[N@@H+]1CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 13, 13, 23, 33, 50, 50, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 23, 23, 50] 50 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: 144 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241285 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `2' /scratch/stefan/7787021/working/building/REAL300025241285/2 /scratch/stefan/7787021/working/building/REAL300025241285 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 2 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/147 `/scratch/stefan/7787021/working/3D/147' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC[N@H+]1CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241285.mol2' -> `2.mol2' `temp.mol2' -> `REAL300025241285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241285/2/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: REAL300025241285 none CC1CC[N@H+]1CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 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, 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: [16, 16, 16, 16, 12, 16, 5, 1, 5, 1, 1, 1, 1, 1, 1, 4, 5, 5, 8, 8, 26, 46, 98, 98, 98, 98, 98, 16, 16, 16, 16, 16, 16, 16, 16, 12, 12, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 26, 26, 98] 129 rigid atoms, others: [43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 270 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241285 none CC1CC[N@H+]1CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 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, 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: [129, 129, 129, 129, 129, 129, 103, 98, 103, 98, 98, 98, 98, 98, 92, 80, 92, 30, 80, 13, 1, 1, 1, 1, 1, 1, 1, 129, 129, 129, 129, 129, 129, 129, 129, 129, 129, 98, 98, 98, 98, 98, 98, 98, 98, 98, 92, 92, 92, 30, 30, 1] 129 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: 485 number of broken/clashed sets: 58 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241285 none CC1CC[N@H+]1CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 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, 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, 1, 1, 1, 4, 10, 10, 16, 16, 16, 16, 16, 18, 19, 19, 26, 26, 53, 76, 129, 129, 129, 129, 129, 2, 2, 2, 1, 1, 1, 1, 1, 4, 4, 16, 16, 16, 16, 16, 16, 16, 18, 18, 19, 19, 19, 53, 53, 129] 129 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: 356 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241285 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241285 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241285/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241285/1.* 2: /scratch/stefan/7787021/working/building/REAL300025241285/2.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241285 Building REAL300025241286 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241286' /scratch/stefan/7787021/working/building/REAL300025241286 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241286 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241286/0 /scratch/stefan/7787021/working/building/REAL300025241286 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/148 `/scratch/stefan/7787021/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C=CC[NH+](C)C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241286.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241286 none CN(CC1CCCN1C(=O)C=CC[NH+](C)C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 41, 41, 41, 41, 24, 38, 13, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 41, 41, 41, 41, 41, 41, 41, 41, 24, 24, 1] 41 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: 138 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: REAL300025241286 none CN(CC1CCCN1C(=O)C=CC[NH+](C)C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 6, 3, 3, 3, 9, 15, 39, 39, 39, 39, 39, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 39] 41 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 100 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241286 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241286 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241286/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241286 Building REAL300025241287 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241287' /scratch/stefan/7787021/working/building/REAL300025241287 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241287 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241287/0 /scratch/stefan/7787021/working/building/REAL300025241287 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/149 `/scratch/stefan/7787021/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CCSC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241287.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241287 none CN(CC1CCCN1C(=O)C1=CCSC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 19, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 25, 47, 47, 82, 125, 201, 201, 201, 201, 201, 25, 25, 25, 19, 19, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 82, 82, 201] 201 rigid atoms, others: [37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44]) total number of confs: 544 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: REAL300025241287 none CN(CC1CCCN1C(=O)C1=CCSC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 109, 117, 153, 156, 156, 156, 156, 156, 172, 172, 201, 201, 201, 201, 41, 109, 13, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 153, 153, 156, 156, 156, 156, 156, 156, 156, 201, 201, 201, 201, 201, 41, 41, 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: 704 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: REAL300025241287 none CN(CC1CCCN1C(=O)C1=CCSC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 1, 5, 5, 11, 11, 11, 11, 9, 17, 17, 33, 59, 156, 156, 156, 156, 156, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 33, 33, 156] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 329 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241287 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241287 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241287/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241287 Building REAL300025241288 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241288' /scratch/stefan/7787021/working/building/REAL300025241288 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241288 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241288/0 /scratch/stefan/7787021/working/building/REAL300025241288 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/150 `/scratch/stefan/7787021/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CCCC(F)F)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241288.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241288 none CN(CC1CCCN1C(=O)CCCC(F)F)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 14, 15, 15, 36, 44, 46, 46, 46, 14, 14, 9, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 36, 36, 46, 46, 46, 46, 46, 14, 14, 1] 46 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: 204 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: REAL300025241288 none CN(CC1CCCN1C(=O)CCCC(F)F)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 10, 12, 16, 16, 3, 4, 4, 7, 9, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 12, 12, 12, 12, 16, 7, 7, 14] 46 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241288 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241288 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241288/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241288 Building REAL300025241289 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241289' /scratch/stefan/7787021/working/building/REAL300025241289 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241289 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241289/0 /scratch/stefan/7787021/working/building/REAL300025241289 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/151 `/scratch/stefan/7787021/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CN1CC(C)(C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241289.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241289 none CN(CC1CCCN1C(=O)CN1CC(C)(C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 15, 7, 7, 7, 7, 7, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 18, 37, 37, 82, 115, 201, 201, 201, 201, 201, 18, 18, 18, 15, 15, 7, 7, 7, 7, 7, 7, 7, 5, 5, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 82, 82, 201] 201 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15, 16, 49, 50, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 51, 52, 53]) total number of confs: 561 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: REAL300025241289 none CN(CC1CCCN1C(=O)CN1CC(C)(C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 72, 107, 133, 146, 146, 146, 146, 146, 146, 146, 201, 201, 201, 201, 201, 201, 25, 72, 13, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 133, 133, 146, 146, 146, 146, 146, 146, 146, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 25, 25, 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: 857 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: REAL300025241289 none CN(CC1CCCN1C(=O)CN1CC(C)(C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 2, 2, 4, 7, 7, 7, 7, 7, 5, 13, 13, 36, 55, 146, 146, 146, 146, 146, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 36, 36, 146] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 329 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241289 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241289/1 /scratch/stefan/7787021/working/building/REAL300025241289 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/152 `/scratch/stefan/7787021/working/3D/152' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C[NH+]1CC(C)(C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241289.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241289/1/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: REAL300025241289 none CN(CC1CCCN1C(=O)C[NH+]1CC(C)(C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 25, 25, 25, 25, 25, 25, 16, 5, 16, 1, 1, 1, 1, 1, 1, 1, 1, 26, 35, 35, 81, 119, 201, 201, 201, 201, 201, 26, 26, 26, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 5, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 81, 81, 201] 201 rigid atoms, others: [43, 10, 11, 12, 13, 14, 15, 16, 17, 50, 51, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 52, 53, 54]) total number of confs: 527 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: REAL300025241289 none CN(CC1CCCN1C(=O)C[NH+]1CC(C)(C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [132, 104, 132, 152, 152, 152, 152, 152, 152, 168, 168, 193, 201, 201, 201, 201, 201, 201, 36, 103, 13, 1, 1, 1, 1, 1, 1, 1, 132, 132, 132, 152, 152, 152, 152, 152, 152, 152, 152, 152, 193, 193, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 36, 36, 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: 764 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: REAL300025241289 none CN(CC1CCCN1C(=O)C[NH+]1CC(C)(C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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 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, 1, 1, 1, 1, 1, 1, 5, 5, 12, 25, 25, 25, 25, 25, 25, 4, 7, 7, 30, 56, 152, 152, 152, 152, 152, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 30, 30, 152] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 39, 34, 35, 36, 38, 37] 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 365 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241289 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241289 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241289/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241289/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241289 Building REAL300025241290 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241290' /scratch/stefan/7787021/working/building/REAL300025241290 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241290 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241290/0 /scratch/stefan/7787021/working/building/REAL300025241290 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/153 `/scratch/stefan/7787021/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241290.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241290 none CO[C@H](C)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 7, 7, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 17, 22, 22, 16, 17, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1] 22 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: 77 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: REAL300025241290 none CO[C@H](C)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 7, 7, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 3, 6, 6, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 7, 9, 16, 16, 16, 16, 16, 7, 7, 7, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 16] 22 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 61 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241290 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241290 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241290/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241290 Building REAL300025241291 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241291' /scratch/stefan/7787021/working/building/REAL300025241291 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241291 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241291/0 /scratch/stefan/7787021/working/building/REAL300025241291 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/154 `/scratch/stefan/7787021/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C12CCC(C1)OC2)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241291.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241291 none CN(CC1CCCN1C(=O)C12CCC(C1)OC2)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 15, 33, 33, 86, 121, 201, 201, 201, 201, 201, 15, 15, 15, 7, 7, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 86, 86, 201] 201 rigid atoms, others: [45, 43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 524 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241291 none CN(CC1CCCN1C(=O)C12CCC(C1)OC2)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 110, 134, 173, 184, 184, 184, 184, 184, 201, 201, 201, 201, 201, 201, 201, 201, 40, 110, 13, 1, 1, 1, 1, 1, 1, 1, 134, 134, 134, 173, 173, 184, 184, 184, 184, 184, 184, 184, 201, 201, 201, 201, 201, 201, 201, 201, 201, 40, 40, 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: 770 number of broken/clashed sets: 127 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241291 none CN(CC1CCCN1C(=O)C12CCC(C1)OC2)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 3, 3, 3, 3, 3, 9, 20, 20, 57, 80, 184, 184, 184, 184, 184, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 57, 57, 184] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 409 number of broken/clashed sets: 127 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241291 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241291 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241291/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241291 Building REAL300025241292 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241292' /scratch/stefan/7787021/working/building/REAL300025241292 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241292 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241292/0 /scratch/stefan/7787021/working/building/REAL300025241292 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/155 `/scratch/stefan/7787021/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1CC12CC(O)C2)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241292.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241292 none CN(CC1CCCN1C(=O)C1CC12CC(O)C2)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 12, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 15, 37, 37, 87, 116, 201, 201, 201, 201, 201, 15, 15, 15, 12, 12, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 1, 1, 87, 87, 201] 603 rigid atoms, others: [43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 48, 49, 50]) total number of confs: 555 number of broken/clashed sets: 210 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241292 none CN(CC1CCCN1C(=O)C1CC12CC(O)C2)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [110, 79, 110, 130, 142, 142, 142, 142, 142, 142, 142, 201, 201, 201, 201, 201, 201, 30, 79, 13, 1, 1, 1, 1, 1, 1, 1, 110, 110, 110, 130, 130, 142, 142, 142, 142, 142, 142, 142, 201, 201, 201, 201, 201, 201, 603, 201, 201, 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: 1333 number of broken/clashed sets: 210 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241292 none CN(CC1CCCN1C(=O)C1CC12CC(O)C2)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [5, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 6, 6, 5, 14, 14, 40, 58, 142, 142, 142, 142, 142, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 18, 6, 6, 40, 40, 142] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 342 number of broken/clashed sets: 210 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241292 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241292 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241292/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241292 Building REAL300025241293 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241293' /scratch/stefan/7787021/working/building/REAL300025241293 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241293 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241293/0 /scratch/stefan/7787021/working/building/REAL300025241293 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/156 `/scratch/stefan/7787021/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C=CC1=NNC=C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241293.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241293 none CN(CC1CCCN1C(=O)C=CC1=NNC=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 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: [20, 18, 10, 10, 10, 10, 10, 8, 4, 7, 4, 1, 1, 1, 1, 1, 1, 20, 35, 35, 86, 125, 201, 201, 201, 201, 201, 20, 20, 20, 18, 18, 10, 10, 10, 10, 10, 10, 10, 4, 4, 1, 1, 1, 86, 86, 201] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46]) total number of confs: 556 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: REAL300025241293 none CN(CC1CCCN1C(=O)C=CC1=NNC=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 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: [141, 99, 141, 158, 174, 174, 174, 174, 174, 195, 195, 201, 201, 201, 201, 201, 201, 28, 99, 13, 1, 1, 1, 1, 1, 1, 1, 141, 141, 141, 158, 158, 174, 174, 174, 174, 174, 174, 174, 201, 201, 201, 201, 201, 28, 28, 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: 686 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: REAL300025241293 none CN(CC1CCCN1C(=O)C=CC1=NNC=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 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: [6, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 10, 10, 10, 10, 6, 12, 12, 34, 62, 174, 174, 174, 174, 174, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 10, 10, 10, 34, 34, 174] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 356 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241293 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241293 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241293/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241293 Building REAL300025241294 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241294' /scratch/stefan/7787021/working/building/REAL300025241294 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241294 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241294/0 /scratch/stefan/7787021/working/building/REAL300025241294 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/157 `/scratch/stefan/7787021/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)C(F)F) `REAL300025241294.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241294 none CC(CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)C(F)F 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 15] 15 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]) total number of confs: 48 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: REAL300025241294 none CC(CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)C(F)F 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 6, 7, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 9, 5] 15 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37] set([0, 1, 2, 4, 11, 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: 48 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241294 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241294 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241294/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241294 Building REAL300025241295 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241295' /scratch/stefan/7787021/working/building/REAL300025241295 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241295 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241295/0 /scratch/stefan/7787021/working/building/REAL300025241295 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/158 `/scratch/stefan/7787021/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C[C@@H]1CCC[C@H]1O)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241295.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241295 none CN(CC1CCCN1C(=O)C[C@@H]1CCC[C@H]1O)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 7, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 12, 15, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 3, 12, 12, 20] 60 rigid atoms, others: [48, 45, 43, 44, 10, 11, 12, 13, 14, 15, 16, 17, 18, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51, 52]) total number of confs: 65 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: REAL300025241295 none CN(CC1CCCN1C(=O)C[C@@H]1CCC[C@H]1O)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 7, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 9, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 60, 11, 11, 1] 60 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: 136 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: REAL300025241295 none CN(CC1CCCN1C(=O)C[C@@H]1CCC[C@H]1O)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 7, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 2, 3, 3, 6, 8, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 12, 6, 6, 11] 60 rigid atoms, others: [2, 3, 4, 5, 6, 7, 40, 39, 34, 8, 35, 36, 38, 37] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 58 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241295 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241295 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241295/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241295 Building REAL300025241296 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241296' /scratch/stefan/7787021/working/building/REAL300025241296 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241296 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241296/0 /scratch/stefan/7787021/working/building/REAL300025241296 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/159 `/scratch/stefan/7787021/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=COC(=O)C=C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241296.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241296 none CN(CC1CCCN1C(=O)C1=COC(=O)C=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 11, 1, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 6, 7, 7, 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: [29, 21, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 29, 57, 57, 102, 131, 201, 201, 201, 201, 201, 29, 29, 29, 21, 21, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 102, 102, 201] 201 rigid atoms, others: [39, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44]) total number of confs: 607 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241296 none CN(CC1CCCN1C(=O)C1=COC(=O)C=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 11, 1, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 6, 7, 7, 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: [86, 86, 86, 114, 117, 117, 117, 117, 117, 138, 138, 201, 201, 201, 201, 201, 201, 38, 86, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 114, 114, 117, 117, 117, 117, 117, 117, 117, 201, 201, 201, 38, 38, 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: 658 number of broken/clashed sets: 60 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241296 none CN(CC1CCCN1C(=O)C1=COC(=O)C=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 11, 1, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 6, 7, 7, 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, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 12, 12, 12, 12, 12, 9, 16, 16, 35, 53, 117, 117, 117, 117, 117, 9, 9, 9, 3, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 35, 35, 117] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44]) total number of confs: 288 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241296 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241296 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241296/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241296 Building REAL300025241297 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241297' /scratch/stefan/7787021/working/building/REAL300025241297 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241297 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241297/0 /scratch/stefan/7787021/working/building/REAL300025241297 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/160 `/scratch/stefan/7787021/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241297.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241297 none CCOC(=O)CCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 5, 7, 7, 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: [201, 201, 201, 109, 201, 71, 45, 45, 45, 45, 45, 45, 45, 44, 39, 31, 39, 16, 31, 11, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 109, 109, 71, 71, 45, 45, 45, 45, 45, 45, 45, 44, 44, 39, 39, 39, 16, 16, 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: 781 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: REAL300025241297 none CCOC(=O)CCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 5, 7, 7, 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: [32, 20, 20, 8, 20, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 4, 4, 9, 9, 15, 21, 45, 45, 45, 45, 45, 32, 32, 32, 32, 32, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 15, 15, 45] 201 rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 237 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241297 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241297 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241297/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241297 Building REAL300025241298 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241298' /scratch/stefan/7787021/working/building/REAL300025241298 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241298 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241298/0 /scratch/stefan/7787021/working/building/REAL300025241298 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/161 `/scratch/stefan/7787021/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)CCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241298.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241298 none CC(=O)CCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 7, 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: [201, 196, 201, 173, 100, 100, 100, 100, 100, 100, 100, 100, 74, 53, 74, 25, 53, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 196, 196, 173, 173, 100, 100, 100, 100, 100, 100, 100, 100, 100, 74, 74, 74, 25, 25, 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: 903 number of broken/clashed sets: 139 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241298 none CC(=O)CCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 7, 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: [21, 10, 21, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 5, 5, 8, 8, 18, 28, 100, 100, 100, 100, 100, 21, 21, 21, 10, 10, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 18, 18, 100] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 255 number of broken/clashed sets: 139 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241298 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241298 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241298/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241298 Building REAL300025241299 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241299' /scratch/stefan/7787021/working/building/REAL300025241299 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241299 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241299/0 /scratch/stefan/7787021/working/building/REAL300025241299 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/162 `/scratch/stefan/7787021/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC1(O)CCCC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241299.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241299 none CN(CC1CCCN1C(=O)CC1(O)CCCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 9, 10, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 11] 33 rigid atoms, others: [48, 45, 43, 44, 10, 11, 12, 13, 14, 15, 16, 49, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 50, 51, 52]) total number of confs: 46 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: REAL300025241299 none CN(CC1CCCN1C(=O)CC1(O)CCCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 11, 11, 8, 8, 7, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 33, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 1] 33 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: 65 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: REAL300025241299 none CN(CC1CCCN1C(=O)CC1(O)CCCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 2, 3, 3, 6, 7, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 8] 33 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 46 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241299 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241299 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241299/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241299 Building REAL300025241300 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241300' /scratch/stefan/7787021/working/building/REAL300025241300 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241300 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241300/0 /scratch/stefan/7787021/working/building/REAL300025241300 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/163 `/scratch/stefan/7787021/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1CCCC1O)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241300.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241300 none CN(CC1CCCN1C(=O)C1CCCC1O)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 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] 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, 12, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 22, 50, 50, 89, 125, 201, 201, 201, 201, 201, 22, 22, 22, 12, 12, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 89, 89, 201] 603 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 44, 40, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 46, 47, 48, 49]) total number of confs: 533 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241300 none CN(CC1CCCN1C(=O)C1CCCC1O)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 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] 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: [142, 113, 142, 184, 192, 192, 192, 192, 192, 201, 201, 201, 201, 201, 201, 201, 41, 113, 13, 1, 1, 1, 1, 1, 1, 1, 142, 142, 142, 184, 184, 192, 192, 192, 192, 192, 192, 192, 201, 201, 201, 201, 201, 201, 201, 201, 603, 41, 41, 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: 1379 number of broken/clashed sets: 176 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241300 none CN(CC1CCCN1C(=O)C1CCCC1O)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 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] 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, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 10, 29, 29, 60, 91, 192, 192, 192, 192, 192, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 18, 60, 60, 192] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 462 number of broken/clashed sets: 176 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241300 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241300 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241300/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241300 Building REAL300025241301 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241301' /scratch/stefan/7787021/working/building/REAL300025241301 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241301 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241301/0 /scratch/stefan/7787021/working/building/REAL300025241301 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/164 `/scratch/stefan/7787021/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241301.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241301 none C[C@@H](O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] 1 hydrogens need rotated 465 conformations in input total number of sets (complete confs): 465 using faster count positions algorithm for large data unique positions, atoms: [155, 144, 155, 155, 143, 144, 143, 143, 143, 143, 142, 110, 99, 110, 40, 99, 13, 1, 1, 1, 1, 1, 1, 1, 155, 155, 155, 465, 143, 143, 143, 143, 143, 143, 143, 142, 142, 110, 110, 110, 40, 40, 1] 465 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: 1073 number of broken/clashed sets: 134 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241301 none C[C@@H](O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] 1 hydrogens need rotated 465 conformations in input total number of sets (complete confs): 465 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 7, 1, 4, 1, 1, 1, 1, 1, 1, 4, 7, 7, 16, 16, 42, 71, 143, 143, 143, 143, 143, 7, 7, 7, 21, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 42, 42, 143] 465 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 376 number of broken/clashed sets: 134 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241301 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241301 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241301/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241301 Building REAL300025241302 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241302' /scratch/stefan/7787021/working/building/REAL300025241302 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241302 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241302/0 /scratch/stefan/7787021/working/building/REAL300025241302 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/165 `/scratch/stefan/7787021/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241302.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241302 none CC[NH+](CC)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 177, 162, 177, 162, 162, 162, 162, 162, 134, 103, 134, 33, 103, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 162, 162, 162, 162, 162, 162, 162, 162, 134, 134, 134, 33, 33, 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: 789 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: REAL300025241302 none CC[NH+](CC)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 13, 12, 13, 13, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 4, 4, 9, 9, 29, 56, 162, 162, 162, 162, 162, 16, 16, 16, 16, 16, 13, 13, 13, 13, 13, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 29, 29, 162] 201 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 41, 7, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 365 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241302 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241302 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241302/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241302 Building REAL300025241303 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241303' /scratch/stefan/7787021/working/building/REAL300025241303 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241303 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241303/0 /scratch/stefan/7787021/working/building/REAL300025241303 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/166 `/scratch/stefan/7787021/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=C1) `REAL300025241303.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241303 none CC1=CC=NC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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: [7, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 7, 7, 14, 14, 41, 62, 144, 144, 144, 144, 144, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 41, 41, 144, 7] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 330 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: REAL300025241303 none CC1=CC=NC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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: [201, 201, 201, 201, 201, 187, 144, 187, 144, 144, 144, 144, 140, 110, 75, 110, 27, 75, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 144, 144, 144, 144, 144, 144, 144, 140, 140, 110, 110, 110, 27, 27, 1, 201] 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]) total number of confs: 725 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: REAL300025241303 none CC1=CC=NC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 13, 19, 19, 35, 35, 81, 108, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 7, 7, 7, 7, 7, 7, 7, 13, 13, 19, 19, 19, 81, 81, 201, 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: 539 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241303 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241303 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241303/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241303 Building REAL300025241304 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241304' /scratch/stefan/7787021/working/building/REAL300025241304 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241304 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241304/0 /scratch/stefan/7787021/working/building/REAL300025241304 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/167 `/scratch/stefan/7787021/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC=C(C#N)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241304.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241304 none CCOC=C(C#N)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 7, 7, 7, 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: [201, 201, 201, 201, 157, 201, 201, 148, 157, 148, 148, 148, 148, 135, 109, 76, 109, 30, 76, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 148, 148, 148, 148, 148, 148, 148, 135, 135, 109, 109, 109, 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: 757 number of broken/clashed sets: 98 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241304 none CCOC=C(C#N)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 7, 7, 7, 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: [11, 11, 8, 8, 3, 8, 8, 1, 3, 1, 1, 1, 1, 1, 1, 4, 7, 7, 12, 12, 29, 46, 148, 148, 148, 148, 148, 11, 11, 11, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 29, 29, 148] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 307 number of broken/clashed sets: 98 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241304 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241304 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241304/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241304 Building REAL300025241305 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241305' /scratch/stefan/7787021/working/building/REAL300025241305 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241305 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241305/0 /scratch/stefan/7787021/working/building/REAL300025241305 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/168 `/scratch/stefan/7787021/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CCC(C)(C)C#N)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241305.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241305 none CN(CC1CCCN1C(=O)CCC(C)(C)C#N)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 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, 16, 16, 16, 16, 16, 16, 16, 16, 16, 30, 30, 33, 33, 33, 33, 16, 16, 10, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 30, 30, 30, 30, 33, 33, 33, 33, 33, 33, 16, 16, 1] 33 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: 128 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: REAL300025241305 none CN(CC1CCCN1C(=O)CCC(C)(C)C#N)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 9, 9, 9, 9, 4, 5, 5, 8, 10, 16, 16, 16, 16, 16, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 8, 8, 16] 33 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241305 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241305 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241305/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241305 Building REAL300025241306 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241306' /scratch/stefan/7787021/working/building/REAL300025241306 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241306 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241306/0 /scratch/stefan/7787021/working/building/REAL300025241306 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/169 `/scratch/stefan/7787021/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CC=C(N)C=N1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241306.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241306 none CN(CC1CCCN1C(=O)C1=CC=C(N)C=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 3, 7, 6, 7, 7, 7, 7, 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: [17, 12, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 17, 33, 33, 79, 107, 201, 201, 201, 201, 201, 17, 17, 17, 12, 12, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 79, 79, 201] 201 rigid atoms, others: [43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 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]) total number of confs: 530 number of broken/clashed sets: 98 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241306 none CN(CC1CCCN1C(=O)C1=CC=C(N)C=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 3, 7, 6, 7, 7, 7, 7, 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: [114, 77, 114, 142, 144, 144, 144, 144, 144, 185, 185, 201, 201, 201, 201, 201, 201, 27, 77, 13, 1, 1, 1, 1, 1, 1, 1, 114, 114, 114, 142, 142, 144, 144, 144, 144, 144, 144, 144, 201, 201, 201, 201, 201, 27, 27, 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: 719 number of broken/clashed sets: 98 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241306 none CN(CC1CCCN1C(=O)C1=CC=C(N)C=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 3, 7, 6, 7, 7, 7, 7, 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, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 7, 14, 14, 41, 62, 144, 144, 144, 144, 144, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 41, 41, 144] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 330 number of broken/clashed sets: 98 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241306 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241306 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241306/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241306 Building REAL300025241307 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241307' /scratch/stefan/7787021/working/building/REAL300025241307 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241307 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241307/0 /scratch/stefan/7787021/working/building/REAL300025241307 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/170 `/scratch/stefan/7787021/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CN1CCC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241307.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241307 none CN(CC1CCCN1C(=O)CN1CCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 8, 11, 13, 16, 16, 16, 16, 16, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 16] 16 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 50 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: REAL300025241307 none CN(CC1CCCN1C(=O)CN1CCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 16, 16, 11, 11, 9, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 11, 11, 1] 16 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: 52 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: REAL300025241307 none CN(CC1CCCN1C(=O)CN1CCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 5, 5, 5, 2, 3, 3, 6, 8, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 6, 6, 11] 16 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 47 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241307 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241307/1 /scratch/stefan/7787021/working/building/REAL300025241307 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/171 `/scratch/stefan/7787021/working/3D/171' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C[NH+]1CCC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241307.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241307/1/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: REAL300025241307 none CN(CC1CCCN1C(=O)C[NH+]1CCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 13, 13, 13, 13, 13, 12, 5, 12, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 13, 13, 13, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 15, 15, 15] 15 rigid atoms, others: [45, 43, 40, 41, 10, 11, 12, 13, 14, 15, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 52 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: REAL300025241307 none CN(CC1CCCN1C(=O)C[NH+]1CCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 14, 14, 8, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15, 14, 14, 1] 15 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: 48 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: REAL300025241307 none CN(CC1CCCN1C(=O)C[NH+]1CCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 13, 13, 13, 13, 4, 5, 5, 6, 8, 14, 14, 14, 14, 14, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 13, 6, 6, 14] 15 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 79 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241307 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241307 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241307/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241307/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241307 Building REAL300025241308 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241308' /scratch/stefan/7787021/working/building/REAL300025241308 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241308 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241308/0 /scratch/stefan/7787021/working/building/REAL300025241308 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/172 `/scratch/stefan/7787021/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(O)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241308.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241308 none CC(C)C(O)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 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, 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, 190, 201, 188, 190, 146, 146, 146, 146, 146, 146, 146, 142, 124, 77, 124, 27, 77, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 190, 570, 188, 188, 146, 146, 146, 146, 146, 146, 146, 142, 142, 124, 124, 124, 27, 27, 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: 1364 number of broken/clashed sets: 351 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241308 none CC(C)C(O)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 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, 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, 10, 14, 7, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 5, 5, 10, 10, 29, 52, 146, 146, 146, 146, 146, 14, 14, 14, 14, 14, 14, 14, 10, 30, 7, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 29, 29, 146] 603 rigid atoms, others: [43, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 371 number of broken/clashed sets: 351 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241308 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241308 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241308/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241308 Building REAL300025241309 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241309' /scratch/stefan/7787021/working/building/REAL300025241309 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241309 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241309/0 /scratch/stefan/7787021/working/building/REAL300025241309 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/173 `/scratch/stefan/7787021/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=C(Cl)CCC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241309.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241309 none CN(CC1CCCN1C(=O)C1=C(Cl)CCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 16, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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] 0 hydrogens 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, 8, 8, 8, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 25, 50, 50, 92, 125, 201, 201, 201, 201, 201, 25, 25, 25, 17, 17, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 92, 92, 201] 201 rigid atoms, others: [43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 576 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241309 none CN(CC1CCCN1C(=O)C1=C(Cl)CCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 16, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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] 0 hydrogens 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, 97, 102, 143, 148, 148, 148, 148, 148, 154, 154, 201, 201, 201, 201, 201, 39, 97, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 102, 143, 143, 148, 148, 148, 148, 148, 148, 148, 201, 201, 201, 201, 201, 201, 39, 39, 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: 686 number of broken/clashed sets: 61 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241309 none CN(CC1CCCN1C(=O)C1=C(Cl)CCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 16, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 10, 20, 20, 42, 67, 148, 148, 148, 148, 148, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 42, 42, 148] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 343 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241309 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241309 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241309/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241309 Building REAL300025241310 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241310' /scratch/stefan/7787021/working/building/REAL300025241310 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241310 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241310/0 /scratch/stefan/7787021/working/building/REAL300025241310 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/174 `/scratch/stefan/7787021/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1COC(=O)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241310.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241310 none CN(CC1CCCN1C(=O)C1COC(=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 1, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 5, 7, 7, 6, 7, 7, 7, 7, 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: [31, 22, 11, 11, 11, 11, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 31, 55, 55, 103, 133, 201, 201, 201, 201, 201, 31, 31, 31, 22, 22, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 103, 103, 201] 201 rigid atoms, others: [38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45]) total number of confs: 599 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: REAL300025241310 none CN(CC1CCCN1C(=O)C1COC(=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 1, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 5, 7, 7, 6, 7, 7, 7, 7, 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, 89, 96, 131, 140, 140, 140, 140, 140, 144, 144, 201, 201, 201, 201, 201, 38, 89, 13, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 131, 131, 140, 140, 140, 140, 140, 140, 140, 201, 201, 201, 201, 201, 38, 38, 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: 788 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: REAL300025241310 none CN(CC1CCCN1C(=O)C1COC(=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 1, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 5, 7, 7, 6, 7, 7, 7, 7, 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, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 9, 21, 21, 50, 73, 140, 140, 140, 140, 140, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 50, 50, 140] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 367 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241310 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241310 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241310/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241310 Building REAL300025241311 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241311' /scratch/stefan/7787021/working/building/REAL300025241311 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241311 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241311/0 /scratch/stefan/7787021/working/building/REAL300025241311 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/175 `/scratch/stefan/7787021/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)CC1) `REAL300025241311.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241311 none CC1CC=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 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, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 6, 6, 17, 17, 49, 75, 180, 180, 180, 180, 180, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 49, 49, 180, 7, 7, 7, 7] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 396 number of broken/clashed sets: 83 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241311 none CC1CC=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 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, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 180, 200, 180, 180, 180, 180, 160, 138, 89, 138, 27, 88, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 180, 180, 180, 180, 180, 180, 180, 160, 160, 138, 138, 138, 27, 27, 1, 201, 201, 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]) total number of confs: 708 number of broken/clashed sets: 83 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241311 none CC1CC=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 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, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 7, 7, 7, 7, 7, 14, 20, 20, 43, 43, 93, 127, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 14, 14, 20, 20, 20, 93, 93, 201, 1, 1, 1, 1] 201 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: 572 number of broken/clashed sets: 83 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241311 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241311 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241311/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241311 Building REAL300025241312 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241312' /scratch/stefan/7787021/working/building/REAL300025241312 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241312 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241312/0 /scratch/stefan/7787021/working/building/REAL300025241312 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/176 `/scratch/stefan/7787021/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(C)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241312.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241312 none CC(O)C(C)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 7, 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] 1 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: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 27, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1] 27 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: 42 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: REAL300025241312 none CC(O)C(C)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 7, 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] 1 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, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 6, 7, 9, 9, 9, 9, 9, 2, 2, 2, 2, 6, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 9] 27 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 39 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241312 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241312 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241312/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241312 Building REAL300025241313 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241313' /scratch/stefan/7787021/working/building/REAL300025241313 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241313 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241313/0 /scratch/stefan/7787021/working/building/REAL300025241313 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/177 `/scratch/stefan/7787021/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CC(=O)N(C)[N-]1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241313.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241313 none CN(CC1CCCN1C(=O)C1=CC(=O)N(C)[N-]1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 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, 26, 15, 15, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 32, 54, 54, 78, 117, 201, 201, 201, 201, 201, 32, 32, 32, 26, 26, 15, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2, 78, 78, 201] 201 rigid atoms, others: [39, 8, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 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]) total number of confs: 527 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: REAL300025241313 none CN(CC1CCCN1C(=O)C1=CC(=O)N(C)[N-]1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 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: [105, 94, 105, 126, 130, 130, 130, 130, 130, 186, 186, 201, 201, 201, 201, 201, 201, 35, 94, 13, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 126, 126, 130, 130, 130, 130, 130, 130, 130, 201, 201, 201, 201, 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: 702 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: REAL300025241313 none CN(CC1CCCN1C(=O)C1=CC(=O)N(C)[N-]1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 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: [6, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 15, 15, 15, 6, 11, 11, 21, 35, 130, 130, 130, 130, 130, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 21, 21, 130] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 256 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241313 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241313 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241313/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241313 Building REAL300025241314 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241314' /scratch/stefan/7787021/working/building/REAL300025241314 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241314 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241314/0 /scratch/stefan/7787021/working/building/REAL300025241314 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/178 `/scratch/stefan/7787021/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241314.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241314 none C=C1CC1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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: [10, 10, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 3, 8, 8, 15, 15, 32, 55, 135, 135, 135, 135, 135, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 8, 8, 32, 32, 135] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 307 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: REAL300025241314 none C=C1CC1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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: [201, 201, 201, 137, 135, 137, 135, 135, 135, 135, 130, 103, 95, 103, 37, 95, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 135, 135, 135, 135, 135, 135, 135, 130, 130, 103, 103, 103, 37, 37, 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: 725 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: REAL300025241314 none C=C1CC1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 1, 7, 7, 10, 10, 10, 10, 10, 18, 25, 25, 49, 49, 85, 122, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 18, 18, 25, 25, 25, 85, 85, 201] 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: 565 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241314 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241314 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241314/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241314 Building REAL300025241315 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241315' /scratch/stefan/7787021/working/building/REAL300025241315 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241315 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241315/0 /scratch/stefan/7787021/working/building/REAL300025241315 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/179 `/scratch/stefan/7787021/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC1CC=CC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241315.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241315 none CN(CC1CCCN1C(=O)CC1CC=CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 1, 1, 1, 1, 1, 1, 7, 10, 10, 21, 24, 28, 28, 28, 28, 28, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 21, 21, 28] 28 rigid atoms, others: [45, 43, 40, 41, 10, 11, 12, 13, 14, 15, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49]) total number of confs: 94 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: REAL300025241315 none CN(CC1CCCN1C(=O)CC1CC=CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 22, 28, 28, 28, 28, 10, 10, 8, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22, 28, 28, 28, 28, 28, 28, 28, 10, 10, 1] 28 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: 103 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: REAL300025241315 none CN(CC1CCCN1C(=O)CC1CC=CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 7, 7, 7, 7, 2, 3, 3, 6, 8, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 10] 28 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241315 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241315 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241315/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241315 Building REAL300025241316 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241316' /scratch/stefan/7787021/working/building/REAL300025241316 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241316 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241316/0 /scratch/stefan/7787021/working/building/REAL300025241316 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/180 `/scratch/stefan/7787021/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC1OCCO1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241316.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241316 none CN(CC1CCCN1C(=O)CC1OCCO1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [9, 9, 9, 9, 9, 9, 9, 7, 3, 7, 1, 1, 1, 1, 1, 1, 9, 12, 12, 18, 19, 22, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 1, 18, 18, 22] 22 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 15, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47]) total number of confs: 73 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: REAL300025241316 none CN(CC1CCCN1C(=O)CC1OCCO1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 22, 11, 11, 1] 22 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: 78 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: REAL300025241316 none CN(CC1CCCN1C(=O)CC1OCCO1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 9, 2, 3, 3, 6, 8, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 6, 6, 11] 22 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 63 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241316 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241316 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241316/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241316 Building REAL300025241317 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241317' /scratch/stefan/7787021/working/building/REAL300025241317 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241317 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241317/0 /scratch/stefan/7787021/working/building/REAL300025241317 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/181 `/scratch/stefan/7787021/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(OC)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241317.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241317 none COC(OC)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 3, 7, 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 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 16, 15, 16, 18, 14, 15, 14, 14, 14, 14, 14, 14, 14, 14, 13, 14, 9, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 16, 18, 18, 18, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 13, 13, 1] 18 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: 56 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: REAL300025241317 none COC(OC)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 3, 7, 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 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 3, 4, 8, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 7, 9, 14, 14, 14, 14, 14, 9, 9, 9, 4, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 14] 18 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 63 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241317 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241317 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241317/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241317 Building REAL300025241318 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241318' /scratch/stefan/7787021/working/building/REAL300025241318 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241318 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241318/0 /scratch/stefan/7787021/working/building/REAL300025241318 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/182 `/scratch/stefan/7787021/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CCC[N+](=O)[O-])C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241318.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241318 none CN(CC1CCCN1C(=O)CCC[N+](=O)[O-])C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 11, 11, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 6, 7, 7, 7, 7, 4, 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 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 33, 34, 44, 44, 44, 15, 15, 9, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 33, 33, 41, 41, 38, 43, 15, 15, 1] 44 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: 213 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: REAL300025241318 none CN(CC1CCCN1C(=O)CCC[N+](=O)[O-])C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 11, 11, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 6, 7, 7, 7, 7, 4, 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 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 9, 14, 17, 17, 3, 4, 4, 7, 9, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 11, 13, 13, 7, 7, 15] 44 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 118 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241318 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241318 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241318/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241318 Building REAL300025241319 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241319' /scratch/stefan/7787021/working/building/REAL300025241319 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241319 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241319/0 /scratch/stefan/7787021/working/building/REAL300025241319 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/183 `/scratch/stefan/7787021/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC1(C#N)CC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241319.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241319 none CN(CC1CCCN1C(=O)CC1(C#N)CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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] 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: [9, 9, 7, 7, 7, 7, 7, 6, 4, 6, 1, 1, 1, 1, 1, 1, 9, 10, 10, 13, 14, 17, 17, 17, 17, 17, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 7, 7, 4, 4, 1, 1, 1, 1, 13, 13, 17] 17 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46]) total number of confs: 57 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: REAL300025241319 none CN(CC1CCCN1C(=O)CC1(C#N)CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 17, 17, 17, 17, 17, 15, 15, 10, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 17, 17, 17, 17, 17, 17, 15, 15, 1] 17 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: 53 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: REAL300025241319 none CN(CC1CCCN1C(=O)CC1(C#N)CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 7, 7, 7, 7, 4, 5, 5, 8, 11, 15, 15, 15, 15, 15, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 8, 8, 15] 17 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 66 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241319 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241319 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241319/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241319 Building REAL300025241320 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241320' /scratch/stefan/7787021/working/building/REAL300025241320 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241320 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241320/0 /scratch/stefan/7787021/working/building/REAL300025241320 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/184 `/scratch/stefan/7787021/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241320.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241320 none COC(=O)CCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 5, 7, 7, 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: [201, 201, 157, 201, 131, 72, 72, 72, 72, 72, 72, 72, 72, 47, 41, 47, 29, 41, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 157, 157, 131, 131, 72, 72, 72, 72, 72, 72, 72, 72, 72, 47, 47, 47, 29, 29, 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: 923 number of broken/clashed sets: 159 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241320 none COC(=O)CCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 5, 7, 7, 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: [23, 23, 9, 23, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 9, 14, 72, 72, 72, 72, 72, 23, 23, 23, 9, 9, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 72] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 190 number of broken/clashed sets: 159 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241320 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241320 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241320/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241320 Building REAL300025241321 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241321' /scratch/stefan/7787021/working/building/REAL300025241321 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241321 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241321/0 /scratch/stefan/7787021/working/building/REAL300025241321 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/185 `/scratch/stefan/7787021/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241321.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241321 none CC[NH+](CC)CCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 52, 56, 56, 56, 52, 48, 41, 48, 41, 41, 41, 41, 41, 41, 38, 41, 23, 38, 13, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 52, 52, 52, 52, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 23, 23, 1] 56 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: 200 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241321 none CC[NH+](CC)CCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [13, 12, 9, 12, 12, 12, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 12, 20, 41, 41, 41, 41, 41, 13, 13, 13, 13, 13, 12, 12, 12, 12, 12, 9, 9, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 41] 56 rigid atoms, others: [43, 15, 8, 44, 10, 11, 12, 13, 14, 45, 48, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 142 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241321 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241321 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241321/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241321 Building REAL300025241322 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241322' /scratch/stefan/7787021/working/building/REAL300025241322 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241322 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241322/0 /scratch/stefan/7787021/working/building/REAL300025241322 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/186 `/scratch/stefan/7787021/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CCCOC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241322.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241322 none CN(CC1CCCN1C(=O)C1=CCCOC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 21, 39, 39, 78, 117, 201, 201, 201, 201, 201, 21, 21, 21, 16, 16, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 78, 78, 201] 201 rigid atoms, others: [43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47]) total number of confs: 538 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241322 none CN(CC1CCCN1C(=O)C1=CCCOC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 88, 92, 124, 125, 125, 125, 125, 125, 132, 132, 201, 201, 201, 201, 201, 38, 88, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 124, 124, 125, 125, 125, 125, 125, 125, 125, 201, 201, 201, 201, 201, 201, 201, 38, 38, 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: 654 number of broken/clashed sets: 61 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241322 none CN(CC1CCCN1C(=O)C1=CCCOC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 7, 13, 13, 31, 50, 125, 125, 125, 125, 125, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 31, 31, 125] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 286 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241322 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241322 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241322/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241322 Building REAL300025241323 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241323' /scratch/stefan/7787021/working/building/REAL300025241323 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241323 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241323/0 /scratch/stefan/7787021/working/building/REAL300025241323 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/187 `/scratch/stefan/7787021/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CN1N=NC(N)=N1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241323.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241323 none CN(CC1CCCN1C(=O)CN1N=NC(N)=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 8, 1, 8, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 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, 20, 20, 20, 20, 9, 20, 1, 1, 1, 1, 1, 1, 1, 32, 40, 40, 74, 109, 201, 201, 201, 201, 201, 32, 32, 32, 32, 32, 20, 20, 20, 20, 20, 20, 20, 9, 9, 1, 1, 74, 74, 201] 201 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15, 16, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 580 number of broken/clashed sets: 141 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241323 none CN(CC1CCCN1C(=O)CN1N=NC(N)=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 8, 1, 8, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 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: [58, 38, 58, 71, 71, 71, 71, 71, 71, 71, 71, 129, 201, 201, 201, 201, 201, 25, 37, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 71, 71, 71, 71, 71, 71, 71, 71, 71, 129, 129, 201, 201, 25, 25, 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: 630 number of broken/clashed sets: 141 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241323 none CN(CC1CCCN1C(=O)CN1N=NC(N)=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 8, 1, 8, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 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: [3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 20, 20, 20, 20, 20, 3, 6, 6, 15, 23, 71, 71, 71, 71, 71, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 15, 15, 71] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 183 number of broken/clashed sets: 141 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241323 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241323 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241323/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241323 Building REAL300025241324 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241324' /scratch/stefan/7787021/working/building/REAL300025241324 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241324 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241324/0 /scratch/stefan/7787021/working/building/REAL300025241324 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/188 `/scratch/stefan/7787021/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=C1) `REAL300025241324.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241324 none CCC1=NOC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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: [10, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 23, 37, 114, 114, 114, 114, 114, 5, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 23, 23, 114, 5] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 257 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: REAL300025241324 none CCC1=NOC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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: [201, 138, 138, 138, 138, 125, 114, 125, 114, 114, 114, 114, 112, 98, 71, 98, 29, 71, 13, 1, 1, 1, 1, 1, 1, 1, 138, 201, 201, 201, 201, 201, 114, 114, 114, 114, 114, 114, 114, 112, 112, 98, 98, 98, 29, 29, 1, 138] 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]) total number of confs: 849 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: REAL300025241324 none CCC1=NOC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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: [4, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 10, 10, 10, 17, 17, 43, 66, 138, 138, 138, 138, 138, 1, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 43, 43, 138, 1] 201 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: 353 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241324 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241324 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241324/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241324 Building REAL300025241325 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241325' /scratch/stefan/7787021/working/building/REAL300025241325 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241325 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241325/0 /scratch/stefan/7787021/working/building/REAL300025241325 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/189 `/scratch/stefan/7787021/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C(O)C(C)(C)C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241325.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241325 none CN(CC1CCCN1C(=O)C(O)C(C)(C)C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 282 conformations in input total number of sets (complete confs): 282 using faster count positions algorithm for large data unique positions, atoms: [67, 61, 67, 83, 84, 84, 84, 84, 84, 94, 94, 94, 94, 94, 94, 94, 33, 61, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 83, 83, 84, 84, 84, 84, 84, 84, 84, 94, 282, 94, 94, 94, 94, 94, 94, 94, 94, 94, 33, 33, 1] 282 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: 640 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: REAL300025241325 none CN(CC1CCCN1C(=O)C(O)C(C)(C)C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 282 conformations in input total number of sets (complete confs): 282 using faster count positions algorithm for large data unique positions, atoms: [8, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 8, 18, 18, 41, 52, 84, 84, 84, 84, 84, 8, 8, 8, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 15, 5, 5, 5, 5, 5, 5, 5, 5, 5, 41, 41, 84] 282 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 258 number of broken/clashed sets: 102 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241325 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241325 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241325/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241325 Building REAL300025241326 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241326' /scratch/stefan/7787021/working/building/REAL300025241326 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241326 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241326/0 /scratch/stefan/7787021/working/building/REAL300025241326 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/190 `/scratch/stefan/7787021/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1CCSCC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241326.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241326 none CN(CC1CCCN1C(=O)C1CCSCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7] 0 hydrogens 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, 15, 8, 8, 8, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 27, 50, 50, 91, 123, 201, 201, 201, 201, 201, 27, 27, 27, 15, 15, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 91, 91, 201] 201 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 538 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241326 none CN(CC1CCCN1C(=O)C1CCSCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7] 0 hydrogens 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, 100, 117, 144, 151, 151, 151, 151, 151, 155, 155, 201, 201, 201, 201, 201, 39, 100, 13, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 144, 144, 151, 151, 151, 151, 151, 151, 151, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 763 number of broken/clashed sets: 67 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241326 none CN(CC1CCCN1C(=O)C1CCSCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 10, 25, 25, 54, 77, 151, 151, 151, 151, 151, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 54, 54, 151] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 376 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241326 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241326 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241326/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241326 Building REAL300025241327 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241327' /scratch/stefan/7787021/working/building/REAL300025241327 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241327 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241327/0 /scratch/stefan/7787021/working/building/REAL300025241327 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/191 `/scratch/stefan/7787021/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C(O)C1CCCC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241327.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241327 none CN(CC1CCCN1C(=O)C(O)C1CCCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 7, 7, 7, 7, 7, 6, 4, 6, 1, 4, 1, 1, 1, 1, 1, 8, 9, 9, 11, 12, 14, 14, 14, 14, 14, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 4, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14] 42 rigid atoms, others: [48, 45, 41, 10, 43, 12, 13, 14, 15, 16, 49, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 60 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: REAL300025241327 none CN(CC1CCCN1C(=O)C(O)C1CCCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 14, 42, 14, 14, 14, 14, 14, 14, 14, 14, 14, 11, 11, 1] 42 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: 84 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: REAL300025241327 none CN(CC1CCCN1C(=O)C(O)C1CCCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 7, 7, 7, 7, 3, 4, 4, 7, 9, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 11] 42 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 72 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241327 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241327 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241327/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241327 Building REAL300025241328 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241328' /scratch/stefan/7787021/working/building/REAL300025241328 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241328 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241328/0 /scratch/stefan/7787021/working/building/REAL300025241328 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/192 `/scratch/stefan/7787021/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CCCCO1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241328.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241328 none CN(CC1CCCN1C(=O)C1=CCCCO1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 13, 13, 13, 13, 13, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 60, 60, 94, 130, 201, 201, 201, 201, 201, 27, 27, 27, 22, 22, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 94, 94, 201] 201 rigid atoms, others: [43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47]) total number of confs: 570 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: REAL300025241328 none CN(CC1CCCN1C(=O)C1=CCCCO1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 92, 99, 131, 136, 136, 136, 136, 136, 168, 168, 201, 201, 201, 201, 201, 38, 92, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 131, 131, 136, 136, 136, 136, 136, 136, 136, 201, 201, 201, 201, 201, 201, 201, 38, 38, 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: 703 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: REAL300025241328 none CN(CC1CCCN1C(=O)C1=CCCCO1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 13, 13, 7, 14, 14, 28, 47, 136, 136, 136, 136, 136, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 28, 28, 136] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 288 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241328 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241328 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241328/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241328 Building REAL300025241329 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241329' /scratch/stefan/7787021/working/building/REAL300025241329 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241329 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241329/0 /scratch/stefan/7787021/working/building/REAL300025241329 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/193 `/scratch/stefan/7787021/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1CC(=O)N1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241329.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241329 none CN(CC1CCCN1C(=O)C1CC(=O)N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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] 0 hydrogens 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, 24, 14, 14, 14, 14, 14, 7, 1, 7, 1, 1, 1, 1, 1, 31, 53, 53, 90, 126, 201, 201, 201, 201, 201, 31, 31, 31, 24, 24, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 90, 90, 201] 201 rigid atoms, others: [37, 38, 39, 8, 10, 11, 12, 13, 14, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43]) total number of confs: 560 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241329 none CN(CC1CCCN1C(=O)C1CC(=O)N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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] 0 hydrogens 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, 90, 93, 126, 133, 133, 133, 133, 133, 135, 135, 201, 201, 201, 201, 39, 90, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 126, 126, 133, 133, 133, 133, 133, 133, 133, 201, 201, 201, 201, 39, 39, 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: 792 number of broken/clashed sets: 61 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241329 none CN(CC1CCCN1C(=O)C1CC(=O)N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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] 0 hydrogens 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, 1, 4, 4, 14, 14, 14, 14, 9, 18, 18, 38, 60, 133, 133, 133, 133, 133, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 38, 38, 133] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 339 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241329 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241329 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241329/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241329 Building REAL300025241330 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241330' /scratch/stefan/7787021/working/building/REAL300025241330 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241330 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241330/0 /scratch/stefan/7787021/working/building/REAL300025241330 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/194 `/scratch/stefan/7787021/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=NOC(CO)=C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241330.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241330 none CN(CC1CCCN1C(=O)C1=NOC(CO)=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 12, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 11, 7, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 8, 1, 13, 20, 20, 49, 80, 201, 201, 201, 201, 201, 13, 13, 13, 11, 11, 7, 7, 7, 7, 7, 7, 7, 8, 8, 26, 1, 49, 49, 201] 603 rigid atoms, others: [8, 10, 11, 12, 13, 14, 16, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 17, 18, 19, 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]) total number of confs: 483 number of broken/clashed sets: 339 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241330 none CN(CC1CCCN1C(=O)C1=NOC(CO)=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 12, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 82, 117, 144, 150, 150, 150, 150, 150, 178, 178, 201, 201, 201, 201, 201, 201, 28, 82, 12, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 144, 144, 150, 150, 150, 150, 150, 150, 150, 201, 201, 603, 201, 28, 28, 1] 603 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: 1308 number of broken/clashed sets: 339 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241330 none CN(CC1CCCN1C(=O)C1=NOC(CO)=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 12, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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: [6, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 18, 7, 6, 11, 11, 30, 53, 150, 150, 150, 150, 150, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 18, 18, 54, 7, 30, 30, 150] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 398 number of broken/clashed sets: 339 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241330 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241330 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241330/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241330 Building REAL300025241331 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241331' /scratch/stefan/7787021/working/building/REAL300025241331 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241331 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241331/0 /scratch/stefan/7787021/working/building/REAL300025241331 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/195 `/scratch/stefan/7787021/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)[C@@H]1CC(=O)N1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241331.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241331 none CN(CC1CCCN1C(=O)[C@@H]1CC(=O)N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 13, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 29, 49, 49, 87, 123, 201, 201, 201, 201, 201, 29, 29, 29, 22, 22, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 87, 87, 201] 201 rigid atoms, others: [38, 39, 8, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43]) total number of confs: 558 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241331 none CN(CC1CCCN1C(=O)[C@@H]1CC(=O)N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 91, 93, 127, 133, 133, 133, 133, 133, 135, 135, 201, 201, 201, 201, 201, 39, 91, 12, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 127, 127, 133, 133, 133, 133, 133, 133, 133, 201, 201, 201, 39, 39, 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: 795 number of broken/clashed sets: 60 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241331 none CN(CC1CCCN1C(=O)[C@@H]1CC(=O)N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 1, 4, 4, 13, 13, 13, 13, 13, 9, 18, 18, 38, 61, 133, 133, 133, 133, 133, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 38, 38, 133] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43]) total number of confs: 338 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241331 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241331 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241331/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241331 Building REAL300025241332 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241332' /scratch/stefan/7787021/working/building/REAL300025241332 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241332 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241332/0 /scratch/stefan/7787021/working/building/REAL300025241332 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/196 `/scratch/stefan/7787021/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CCCCC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241332.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241332 none CN(CC1CCCN1C(=O)C1=CCCCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 22, 45, 45, 88, 123, 201, 201, 201, 201, 201, 22, 22, 22, 16, 16, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 88, 88, 201] 201 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 567 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: REAL300025241332 none CN(CC1CCCN1C(=O)C1=CCCCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7] 0 hydrogens 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, 107, 117, 156, 166, 166, 166, 166, 166, 187, 187, 201, 201, 201, 201, 201, 40, 107, 13, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 156, 156, 166, 166, 166, 166, 166, 166, 166, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 744 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: REAL300025241332 none CN(CC1CCCN1C(=O)C1=CCCCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 7, 13, 13, 32, 56, 166, 166, 166, 166, 166, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 32, 32, 166] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 339 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241332 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241332 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241332/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241332 Building REAL300025241333 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241333' /scratch/stefan/7787021/working/building/REAL300025241333 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241333 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241333/0 /scratch/stefan/7787021/working/building/REAL300025241333 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/197 `/scratch/stefan/7787021/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CN(C)N=C1N)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241333.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241333 none CN(CC1CCCN1C(=O)C1=CN(C)N=C1N)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 15, 15, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 32, 54, 54, 85, 118, 201, 201, 201, 201, 201, 32, 32, 32, 27, 27, 15, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2, 1, 1, 85, 85, 201] 201 rigid atoms, others: [43, 39, 8, 44, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 45, 46, 47]) total number of confs: 565 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: REAL300025241333 none CN(CC1CCCN1C(=O)C1=CN(C)N=C1N)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 88, 89, 117, 122, 122, 122, 122, 122, 156, 156, 201, 201, 201, 201, 201, 201, 37, 88, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 117, 117, 122, 122, 122, 122, 122, 122, 122, 201, 201, 201, 201, 201, 201, 37, 37, 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: 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: REAL300025241333 none CN(CC1CCCN1C(=O)C1=CN(C)N=C1N)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 15, 15, 15, 6, 12, 12, 24, 41, 122, 122, 122, 122, 122, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 24, 24, 122] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 265 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241333 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241333 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241333/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241333 Building REAL300025241334 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241334' /scratch/stefan/7787021/working/building/REAL300025241334 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241334 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241334/0 /scratch/stefan/7787021/working/building/REAL300025241334 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/198 `/scratch/stefan/7787021/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241334.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241334 none CCC[C@H](O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 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] 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, 148, 92, 148, 148, 84, 92, 84, 84, 84, 84, 83, 71, 51, 71, 24, 50, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 444, 84, 84, 84, 84, 84, 84, 84, 83, 83, 71, 71, 71, 24, 24, 1] 603 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: 1377 number of broken/clashed sets: 349 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241334 none CCC[C@H](O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 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] 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, 6, 3, 6, 6, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 19, 31, 84, 84, 84, 84, 84, 11, 11, 11, 11, 11, 11, 11, 18, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 19, 19, 84] 603 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 238 number of broken/clashed sets: 349 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241334 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241334 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241334/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241334 Building REAL300025241335 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241335' /scratch/stefan/7787021/working/building/REAL300025241335 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241335 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241335/0 /scratch/stefan/7787021/working/building/REAL300025241335 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/199 `/scratch/stefan/7787021/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC1COCCO1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241335.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241335 none CN(CC1CCCN1C(=O)CC1COCCO1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 6, 6, 6, 6, 6, 6, 4, 6, 1, 1, 1, 1, 1, 1, 1, 12, 27, 27, 71, 108, 201, 201, 201, 201, 201, 12, 12, 12, 10, 10, 6, 6, 6, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 71, 71, 201] 201 rigid atoms, others: [45, 43, 41, 10, 11, 12, 13, 14, 15, 16, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50]) total number of confs: 524 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241335 none CN(CC1CCCN1C(=O)CC1COCCO1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 75, 106, 125, 131, 131, 131, 131, 131, 131, 131, 201, 201, 201, 201, 201, 201, 29, 74, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 125, 125, 131, 131, 131, 131, 131, 131, 131, 201, 201, 201, 201, 201, 201, 201, 201, 201, 29, 29, 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: 860 number of broken/clashed sets: 70 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241335 none CN(CC1CCCN1C(=O)CC1COCCO1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 2, 2, 5, 6, 6, 6, 6, 6, 5, 12, 12, 31, 48, 131, 131, 131, 131, 131, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 6, 6, 31, 31, 131] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 289 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241335 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241335 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241335/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241335 Building REAL300025241336 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241336' /scratch/stefan/7787021/working/building/REAL300025241336 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241336 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241336/0 /scratch/stefan/7787021/working/building/REAL300025241336 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/200 `/scratch/stefan/7787021/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CN1N=CC=C1N)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241336.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241336 none CN(CC1CCCN1C(=O)CN1N=CC=C1N)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 8, 8, 8, 8, 6, 4, 6, 1, 1, 1, 1, 1, 1, 1, 9, 13, 13, 18, 22, 24, 24, 24, 24, 24, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 8, 4, 4, 1, 1, 1, 1, 18, 18, 24] 24 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 15, 16, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47]) total number of confs: 83 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: REAL300025241336 none CN(CC1CCCN1C(=O)CN1N=CC=C1N)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 24, 24, 24, 24, 24, 24, 15, 15, 9, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 24, 24, 24, 24, 24, 24, 15, 15, 1] 24 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: 94 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: REAL300025241336 none CN(CC1CCCN1C(=O)CN1N=CC=C1N)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 8, 8, 8, 8, 8, 3, 4, 4, 7, 9, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 7, 7, 15] 24 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 61 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241336 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241336 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241336/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241336 Building REAL300025241337 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241337' /scratch/stefan/7787021/working/building/REAL300025241337 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241337 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241337/0 /scratch/stefan/7787021/working/building/REAL300025241337 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/201 `/scratch/stefan/7787021/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=CN1) `REAL300025241337.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241337 none CCC1=NC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=CN1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [17, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 4, 4, 7, 7, 15, 25, 102, 102, 102, 102, 102, 5, 5, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 15, 15, 102, 5, 5] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 232 number of broken/clashed sets: 142 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241337 none CCC1=NC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=CN1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 150, 150, 150, 133, 102, 133, 102, 102, 102, 102, 98, 69, 60, 69, 30, 60, 13, 1, 1, 1, 1, 1, 1, 1, 150, 150, 201, 201, 201, 201, 201, 102, 102, 102, 102, 102, 102, 102, 98, 98, 69, 69, 69, 30, 30, 1, 150, 150] 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]) total number of confs: 876 number of broken/clashed sets: 142 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241337 none CCC1=NC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=CN1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [6, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 9, 11, 11, 15, 15, 36, 57, 150, 150, 150, 150, 150, 1, 1, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 9, 9, 11, 11, 11, 36, 36, 150, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 47, 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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 345 number of broken/clashed sets: 142 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241337 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241337/1 /scratch/stefan/7787021/working/building/REAL300025241337 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/202 `/scratch/stefan/7787021/working/3D/202' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)N1) `REAL300025241337.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241337/1/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: REAL300025241337 none CCC1=NC=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 9, 14, 53, 53, 53, 53, 53, 7, 16, 16, 16, 16, 16, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 53, 7] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 152 number of broken/clashed sets: 158 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241337 none CCC1=NC=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 84, 53, 84, 53, 53, 53, 53, 53, 34, 30, 34, 20, 29, 11, 1, 1, 1, 1, 1, 1, 1, 144, 201, 201, 201, 201, 201, 144, 53, 53, 53, 53, 53, 53, 53, 53, 53, 34, 34, 34, 20, 20, 1, 144] 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]) total number of confs: 792 number of broken/clashed sets: 158 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241337 none CCC1=NC=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 11, 11, 11, 13, 13, 33, 51, 144, 144, 144, 144, 144, 1, 6, 6, 6, 6, 6, 1, 7, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 33, 33, 144, 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: 331 number of broken/clashed sets: 158 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241337 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241337 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241337/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241337/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241337 Building REAL300025241338 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241338' /scratch/stefan/7787021/working/building/REAL300025241338 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241338 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241338/0 /scratch/stefan/7787021/working/building/REAL300025241338 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/203 `/scratch/stefan/7787021/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=NN1) `REAL300025241338.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241338 none CCC1=NC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=NN1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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: [18, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 4, 4, 5, 5, 10, 17, 79, 79, 79, 79, 79, 6, 6, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 10, 10, 79, 6] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 192 number of broken/clashed sets: 159 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241338 none CCC1=NC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=NN1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 151, 151, 151, 95, 79, 95, 79, 79, 79, 79, 79, 55, 46, 55, 27, 46, 13, 1, 1, 1, 1, 1, 1, 1, 151, 151, 201, 201, 201, 201, 201, 79, 79, 79, 79, 79, 79, 79, 79, 79, 55, 55, 55, 27, 27, 1, 151] 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]) total number of confs: 799 number of broken/clashed sets: 159 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241338 none CCC1=NC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=NN1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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: [7, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 9, 10, 10, 13, 13, 32, 50, 151, 151, 151, 151, 151, 1, 1, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 9, 9, 10, 10, 10, 32, 32, 151, 1] 201 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: 329 number of broken/clashed sets: 159 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241338 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241338/1 /scratch/stefan/7787021/working/building/REAL300025241338 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/204 `/scratch/stefan/7787021/working/3D/204' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NNC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=N1) `REAL300025241338.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241338/1/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: REAL300025241338 none CCC1=NNC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 4, 7, 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: [13, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 6, 6, 9, 9, 19, 34, 87, 87, 87, 87, 87, 6, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 19, 19, 87] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 222 number of broken/clashed sets: 114 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241338 none CCC1=NNC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 4, 7, 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: [201, 116, 116, 116, 116, 113, 87, 113, 87, 87, 87, 87, 85, 71, 51, 71, 24, 51, 12, 1, 1, 1, 1, 1, 1, 1, 116, 201, 201, 201, 201, 201, 116, 87, 87, 87, 87, 87, 87, 87, 85, 85, 71, 71, 71, 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: 926 number of broken/clashed sets: 114 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241338 none CCC1=NNC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 4, 7, 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: [5, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 10, 12, 12, 18, 18, 37, 59, 116, 116, 116, 116, 116, 1, 5, 5, 5, 5, 5, 1, 6, 6, 6, 6, 6, 6, 6, 10, 10, 12, 12, 12, 37, 37, 116] 201 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: 304 number of broken/clashed sets: 114 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241338 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241338 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241338/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241338/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241338 Building REAL300025241339 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241339' /scratch/stefan/7787021/working/building/REAL300025241339 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241339 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241339/0 /scratch/stefan/7787021/working/building/REAL300025241339 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/205 `/scratch/stefan/7787021/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC1(O)CCOC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241339.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241339 none CN(CC1CCCN1C(=O)CC1(O)CCOC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7] 21 rigid atoms, others: [45, 43, 44, 10, 11, 12, 13, 14, 15, 16, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 31 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: REAL300025241339 none CN(CC1CCCN1C(=O)CC1(O)CCOC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 7, 7, 7, 7, 7, 7, 7, 7, 1] 21 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: 29 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: REAL300025241339 none CN(CC1CCCN1C(=O)CC1(O)CCOC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 2, 2, 2, 5, 6, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 3, 3, 3, 3, 3, 3, 5, 5, 7] 21 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 42 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241339 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241339 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241339/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241339 Building REAL300025241340 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241340' /scratch/stefan/7787021/working/building/REAL300025241340 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241340 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241340/0 /scratch/stefan/7787021/working/building/REAL300025241340 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/206 `/scratch/stefan/7787021/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC1=NC=NN1C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241340.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241340 none CN(CC1CCCN1C(=O)CC1=NC=NN1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 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] 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, 6, 6, 6, 6, 6, 5, 3, 5, 1, 1, 1, 1, 1, 1, 1, 7, 9, 9, 12, 15, 22, 22, 22, 22, 22, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 2, 2, 2, 12, 12, 22] 22 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 69 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: REAL300025241340 none CN(CC1CCCN1C(=O)CC1=NC=NN1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 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] 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: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 22, 22, 22, 22, 22, 22, 18, 18, 10, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 22, 22, 22, 22, 22, 22, 18, 18, 1] 22 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: 80 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: REAL300025241340 none CN(CC1CCCN1C(=O)CC1=NC=NN1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 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] 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: [4, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 4, 5, 5, 8, 11, 18, 18, 18, 18, 18, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 8, 8, 18] 22 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 66 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241340 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241340 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241340/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241340 Building REAL300025241341 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241341' /scratch/stefan/7787021/working/building/REAL300025241341 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241341 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241341/0 /scratch/stefan/7787021/working/building/REAL300025241341 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/207 `/scratch/stefan/7787021/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=N1) `REAL300025241341.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241341 none CC1=NN(C)C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 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, 7, 7, 7, 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: [6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 8, 8, 18, 18, 49, 79, 152, 152, 152, 152, 152, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 49, 49, 152] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 373 number of broken/clashed sets: 73 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241341 none CC1=NN(C)C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 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, 7, 7, 7, 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: [201, 201, 201, 201, 201, 153, 152, 153, 152, 152, 152, 152, 150, 104, 67, 104, 27, 67, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 152, 152, 152, 152, 152, 152, 152, 150, 150, 104, 104, 104, 27, 27, 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: 687 number of broken/clashed sets: 73 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241341 none CC1=NN(C)C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 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, 7, 7, 7, 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, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 9, 15, 15, 29, 29, 76, 115, 201, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 9, 9, 15, 15, 15, 76, 76, 201] 201 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: 526 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241341 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241341 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241341/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241341 Building REAL300025241342 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241342' /scratch/stefan/7787021/working/building/REAL300025241342 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241342 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241342/0 /scratch/stefan/7787021/working/building/REAL300025241342 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/208 `/scratch/stefan/7787021/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)[NH+]1CCC1) `REAL300025241342.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241342 none CC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)[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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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 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, 128, 128, 128, 128, 126, 108, 89, 108, 31, 88, 13, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 128, 128, 128, 128, 128, 128, 128, 128, 128, 128, 128, 128, 128, 126, 126, 108, 108, 108, 31, 31, 1, 128, 128, 128, 128, 128, 128] 128 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]) total number of confs: 446 number of broken/clashed sets: 66 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241342 none CC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)[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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 7, 7, 10, 10, 10, 10, 10, 12, 16, 16, 22, 22, 48, 74, 128, 128, 128, 128, 128, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 12, 12, 16, 16, 16, 48, 48, 128, 1, 1, 1, 1, 1, 1] 128 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: 324 number of broken/clashed sets: 66 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241342 none CC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)[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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 8, 8, 13, 13, 37, 62, 128, 128, 128, 128, 128, 7, 10, 10, 10, 10, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 37, 37, 128, 10, 10, 10, 10, 10, 10] 128 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 37, 31] set([0, 1, 3, 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]) total number of confs: 318 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241342 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241342/1 /scratch/stefan/7787021/working/building/REAL300025241342 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/209 `/scratch/stefan/7787021/working/3D/209' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)N1CCC1) `REAL300025241342.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241342/1/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: REAL300025241342 none CC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 182, 196, 182, 182, 182, 182, 177, 145, 94, 145, 30, 94, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 182, 182, 182, 182, 182, 182, 182, 177, 177, 145, 145, 145, 30, 30, 1, 201, 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]) total number of confs: 750 number of broken/clashed sets: 93 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241342 none CC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 8, 8, 8, 8, 8, 15, 19, 19, 37, 37, 86, 123, 201, 201, 201, 201, 201, 1, 1, 1, 1, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 15, 15, 19, 19, 19, 86, 86, 201, 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: 562 number of broken/clashed sets: 93 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241342 none CC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 4, 6, 6, 15, 15, 46, 74, 182, 182, 182, 182, 182, 6, 8, 8, 8, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 46, 46, 182, 8, 8, 8, 8, 8, 8] 201 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 30, 31] set([0, 1, 3, 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]) total number of confs: 410 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241342 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241342 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241342/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241342/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241342 Building REAL300025241343 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241343' /scratch/stefan/7787021/working/building/REAL300025241343 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241343 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241343/0 /scratch/stefan/7787021/working/building/REAL300025241343 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/210 `/scratch/stefan/7787021/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CC=C(N)C=C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241343.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241343 none CN(CC1CCCN1C(=O)C1=CC=C(N)C=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [18, 13, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 18, 42, 42, 82, 112, 201, 201, 201, 201, 201, 18, 18, 18, 13, 13, 6, 6, 6, 6, 6, 6, 6, 1, 1, 2, 2, 1, 1, 82, 82, 201] 201 rigid atoms, others: [43, 39, 8, 44, 10, 11, 12, 13, 14, 15, 16, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 45, 46, 47]) total number of confs: 539 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: REAL300025241343 none CN(CC1CCCN1C(=O)C1=CC=C(N)C=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [140, 98, 140, 165, 177, 177, 177, 177, 177, 201, 201, 201, 201, 201, 201, 201, 201, 30, 98, 13, 1, 1, 1, 1, 1, 1, 1, 140, 140, 140, 165, 165, 177, 177, 177, 177, 177, 177, 177, 201, 201, 201, 201, 201, 201, 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: 706 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: REAL300025241343 none CN(CC1CCCN1C(=O)C1=CC=C(N)C=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [6, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 18, 18, 50, 79, 177, 177, 177, 177, 177, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 50, 50, 177] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 403 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241343 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241343 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241343/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241343 Building REAL300025241344 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241344' /scratch/stefan/7787021/working/building/REAL300025241344 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241344 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241344/0 /scratch/stefan/7787021/working/building/REAL300025241344 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/211 `/scratch/stefan/7787021/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)[C@H]1CC1(F)F)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241344.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241344 none CN(CC1CCCN1C(=O)[C@H]1CC1(F)F)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 25, 15, 15, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 35, 55, 55, 95, 128, 201, 201, 201, 201, 201, 35, 35, 35, 25, 25, 15, 15, 15, 15, 15, 15, 15, 1, 1, 95, 95, 201] 201 rigid atoms, others: [38, 39, 8, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 565 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: REAL300025241344 none CN(CC1CCCN1C(=O)[C@H]1CC1(F)F)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 100, 109, 143, 146, 146, 146, 146, 146, 150, 150, 201, 201, 201, 201, 201, 41, 100, 12, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 143, 143, 146, 146, 146, 146, 146, 146, 146, 201, 201, 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: 748 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: REAL300025241344 none CN(CC1CCCN1C(=O)[C@H]1CC1(F)F)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 1, 5, 5, 15, 15, 15, 15, 15, 9, 18, 18, 41, 64, 146, 146, 146, 146, 146, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 41, 41, 146] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42]) total number of confs: 356 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241344 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241344 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241344/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241344 Building REAL300025241345 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241345' /scratch/stefan/7787021/working/building/REAL300025241345 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241345 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241345/0 /scratch/stefan/7787021/working/building/REAL300025241345 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/212 `/scratch/stefan/7787021/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC1=CNN=C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241345.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241345 none CN(CC1CCCN1C(=O)CC1=CNN=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 8, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 9, 9, 9, 9, 9, 8, 6, 8, 1, 1, 1, 1, 1, 1, 10, 11, 11, 17, 17, 21, 21, 21, 21, 21, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 17, 17, 21] 21 rigid atoms, others: [40, 41, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45]) total number of confs: 76 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: REAL300025241345 none CN(CC1CCCN1C(=O)CC1=CNN=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 8, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 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 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 23, 23, 23, 23, 23, 10, 10, 8, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 23, 23, 23, 23, 23, 10, 10, 1] 23 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: 81 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: REAL300025241345 none CN(CC1CCCN1C(=O)CC1=CNN=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 8, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 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 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 9, 9, 9, 9, 2, 3, 3, 6, 8, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 8, 8, 9, 9, 9, 6, 6, 10] 23 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 60 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241345 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241345 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241345/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241345 Building REAL300025241346 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241346' /scratch/stefan/7787021/working/building/REAL300025241346 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241346 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241346/0 /scratch/stefan/7787021/working/building/REAL300025241346 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/213 `/scratch/stefan/7787021/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)N=C1) `REAL300025241346.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241346 none CC1=CC=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 7, 7, 14, 14, 41, 64, 142, 142, 142, 142, 142, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 41, 41, 142, 7] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 329 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241346 none CC1=CC=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 142, 185, 142, 142, 142, 142, 139, 112, 77, 112, 28, 77, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 142, 142, 142, 142, 142, 142, 142, 139, 139, 112, 112, 112, 28, 28, 1, 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]) total number of confs: 721 number of broken/clashed sets: 102 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241346 none CC1=CC=C(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 4, 4, 7, 7, 7, 7, 7, 12, 16, 16, 31, 31, 77, 106, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 7, 7, 7, 7, 7, 7, 7, 12, 12, 16, 16, 16, 77, 77, 201, 1] 201 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: 527 number of broken/clashed sets: 102 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241346 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241346 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241346/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241346 Building REAL300025241347 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241347' /scratch/stefan/7787021/working/building/REAL300025241347 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241347 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241347/0 /scratch/stefan/7787021/working/building/REAL300025241347 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/214 `/scratch/stefan/7787021/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC1=CC(=O)NN1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241347.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241347 none CN(CC1CCCN1C(=O)CC1=CC(=O)NN1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 11, 8, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 17, 22, 22, 32, 34, 43, 43, 43, 43, 43, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 1, 1, 1, 32, 32, 43] 43 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 15, 16, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46]) total number of confs: 143 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: REAL300025241347 none CN(CC1CCCN1C(=O)CC1=CC(=O)NN1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 11, 8, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 14, 15, 15, 35, 43, 43, 43, 43, 43, 14, 14, 10, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 35, 35, 43, 43, 43, 14, 14, 1] 43 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: 142 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: REAL300025241347 none CN(CC1CCCN1C(=O)CC1=CC(=O)NN1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 11, 8, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 17, 17, 17, 17, 3, 4, 4, 7, 10, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 17, 17, 17, 7, 7, 14] 43 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 85 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241347 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241347 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241347/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241347 Building REAL300025241348 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241348' /scratch/stefan/7787021/working/building/REAL300025241348 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241348 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241348/0 /scratch/stefan/7787021/working/building/REAL300025241348 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/215 `/scratch/stefan/7787021/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C(O)CC(C)(C)C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241348.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241348 none CN(CC1CCCN1C(=O)C(O)CC(C)(C)C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 22, 22, 22, 22, 22, 22, 15, 15, 10, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 22, 66, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 15, 15, 1] 66 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: 140 number of broken/clashed sets: 66 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241348 none CN(CC1CCCN1C(=O)C(O)CC(C)(C)C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 3, 4, 4, 7, 9, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 15, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 15] 66 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 70 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241348 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241348 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241348/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241348 Building REAL300025241349 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241349' /scratch/stefan/7787021/working/building/REAL300025241349 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241349 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241349/0 /scratch/stefan/7787021/working/building/REAL300025241349 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/216 `/scratch/stefan/7787021/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC1=CNC=C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241349.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241349 none CN(CC1CCCN1C(=O)CC1=CNC=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 8, 8, 8, 8, 8, 7, 6, 7, 1, 1, 1, 1, 1, 1, 9, 13, 13, 25, 27, 31, 31, 31, 31, 31, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 8, 6, 6, 1, 1, 1, 1, 25, 25, 31] 31 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46]) total number of confs: 113 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: REAL300025241349 none CN(CC1CCCN1C(=O)CC1=CNC=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 22, 31, 31, 31, 31, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 31, 31, 31, 31, 11, 11, 1] 31 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: 97 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: REAL300025241349 none CN(CC1CCCN1C(=O)CC1=CNC=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 8, 8, 8, 8, 3, 4, 4, 7, 9, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 7, 7, 11] 31 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 56 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241349 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241349 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241349/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241349 Building REAL300025241350 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241350' /scratch/stefan/7787021/working/building/REAL300025241350 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241350 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241350/0 /scratch/stefan/7787021/working/building/REAL300025241350 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/217 `/scratch/stefan/7787021/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241350.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241350 none COC(=O)C(C)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 5, 7, 7, 7, 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: [201, 201, 153, 201, 132, 153, 95, 95, 95, 95, 95, 95, 95, 95, 76, 52, 76, 23, 52, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 153, 153, 153, 153, 132, 132, 95, 95, 95, 95, 95, 95, 95, 95, 95, 76, 76, 76, 23, 23, 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: 819 number of broken/clashed sets: 117 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241350 none COC(=O)C(C)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 5, 7, 7, 7, 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: [18, 18, 10, 18, 6, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 21, 31, 95, 95, 95, 95, 95, 18, 18, 18, 10, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 21, 21, 95] 201 rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 257 number of broken/clashed sets: 117 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241350 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241350 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241350/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241350 Building REAL300025241351 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241351' /scratch/stefan/7787021/working/building/REAL300025241351 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241351 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241351/0 /scratch/stefan/7787021/working/building/REAL300025241351 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/218 `/scratch/stefan/7787021/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1CCC(C)(C)O1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241351.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241351 none CN(CC1CCCN1C(=O)C1CCC(C)(C)O1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 9, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 21, 43, 43, 85, 124, 201, 201, 201, 201, 201, 21, 21, 21, 17, 17, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 85, 85, 201] 201 rigid atoms, others: [43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 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: 564 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: REAL300025241351 none CN(CC1CCCN1C(=O)C1CCC(C)(C)O1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 108, 122, 154, 159, 159, 159, 159, 159, 177, 177, 201, 201, 201, 201, 201, 201, 41, 108, 13, 1, 1, 1, 1, 1, 1, 1, 122, 122, 122, 154, 154, 159, 159, 159, 159, 159, 159, 159, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 760 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: REAL300025241351 none CN(CC1CCCN1C(=O)C1CCC(C)(C)O1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 9, 9, 7, 12, 12, 35, 64, 159, 159, 159, 159, 159, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 35, 35, 159] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 345 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241351 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241351 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241351/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241351 Building REAL300025241352 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241352' /scratch/stefan/7787021/working/building/REAL300025241352 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241352 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241352/0 /scratch/stefan/7787021/working/building/REAL300025241352 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/219 `/scratch/stefan/7787021/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC1=CC=NN1C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241352.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241352 none CN(CC1CCCN1C(=O)CC1=CC=NN1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 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] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 6, 6, 6, 6, 6, 6, 3, 6, 1, 1, 1, 1, 1, 1, 1, 9, 10, 10, 14, 16, 18, 18, 18, 18, 18, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 1, 2, 2, 2, 14, 14, 18] 18 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15, 16, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48]) total number of confs: 74 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: REAL300025241352 none CN(CC1CCCN1C(=O)CC1=CC=NN1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 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] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 18, 18, 18, 18, 18, 18, 14, 14, 9, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 18, 18, 18, 18, 18, 18, 18, 14, 14, 1] 18 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: 61 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: REAL300025241352 none CN(CC1CCCN1C(=O)CC1=CC=NN1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 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] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 6, 6, 4, 5, 5, 8, 11, 14, 14, 14, 14, 14, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 8, 8, 14] 18 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 61 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241352 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241352 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241352/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241352 Building REAL300025241353 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241353' /scratch/stefan/7787021/working/building/REAL300025241353 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241353 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241353/0 /scratch/stefan/7787021/working/building/REAL300025241353 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/220 `/scratch/stefan/7787021/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC1CC(=O)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241353.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241353 none CN(CC1CCCN1C(=O)CC1CC(=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [10, 10, 8, 8, 8, 8, 8, 8, 4, 8, 1, 1, 1, 1, 1, 1, 10, 14, 14, 21, 23, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 8, 8, 8, 8, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 21, 21, 26] 26 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 15, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47]) total number of confs: 98 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: REAL300025241353 none CN(CC1CCCN1C(=O)CC1CC(=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 20, 26, 26, 26, 26, 12, 12, 8, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 20, 20, 26, 26, 26, 26, 26, 12, 12, 1] 26 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: 96 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: REAL300025241353 none CN(CC1CCCN1C(=O)CC1CC(=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 1, 1, 1, 1, 1, 1, 3, 3, 6, 8, 8, 8, 8, 3, 4, 4, 7, 9, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 7, 7, 12] 26 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 62 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241353 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241353 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241353/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241353 Building REAL300025241354 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241354' /scratch/stefan/7787021/working/building/REAL300025241354 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241354 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241354/0 /scratch/stefan/7787021/working/building/REAL300025241354 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/221 `/scratch/stefan/7787021/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC1CSC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241354.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241354 none CN(CC1CCCN1C(=O)CC1CSC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 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: [11, 11, 11, 11, 11, 11, 11, 11, 4, 11, 1, 1, 1, 1, 1, 11, 13, 13, 19, 21, 24, 24, 24, 24, 24, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 19, 19, 24] 24 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46]) total number of confs: 81 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: REAL300025241354 none CN(CC1CCCN1C(=O)CC1CSC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 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, 12, 12, 12, 12, 12, 12, 12, 13, 13, 21, 24, 24, 24, 12, 12, 8, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 21, 21, 24, 24, 24, 24, 24, 12, 12, 1] 24 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: 91 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: REAL300025241354 none CN(CC1CCCN1C(=O)CC1CSC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 11, 11, 11, 3, 4, 4, 7, 9, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 7, 7, 12] 24 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 73 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241354 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241354 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241354/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241354 Building REAL300025241355 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241355' /scratch/stefan/7787021/working/building/REAL300025241355 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241355 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241355/0 /scratch/stefan/7787021/working/building/REAL300025241355 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/222 `/scratch/stefan/7787021/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CNC=N1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241355.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241355 none CN(CC1CCCN1C(=O)C1=CNC=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 6, 7, 7, 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 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [25, 20, 10, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 1, 1, 25, 48, 48, 65, 91, 153, 153, 153, 153, 153, 25, 25, 25, 20, 20, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 65, 65, 153] 153 rigid atoms, others: [37, 38, 39, 8, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42]) total number of confs: 417 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: REAL300025241355 none CN(CC1CCCN1C(=O)C1=CNC=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 6, 7, 7, 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 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [101, 89, 101, 126, 129, 129, 129, 129, 129, 153, 153, 153, 153, 153, 153, 39, 89, 13, 1, 1, 1, 1, 1, 1, 1, 101, 101, 101, 126, 126, 129, 129, 129, 129, 129, 129, 129, 153, 153, 153, 39, 39, 1] 153 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: 584 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: REAL300025241355 none CN(CC1CCCN1C(=O)C1=CNC=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 6, 7, 7, 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 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 7, 13, 13, 21, 39, 129, 129, 129, 129, 129, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 21, 21, 129] 153 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 251 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241355 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241355/1 /scratch/stefan/7787021/working/building/REAL300025241355 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/223 `/scratch/stefan/7787021/working/3D/223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CN=CN1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241355.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241355/1/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: REAL300025241355 none CN(CC1CCCN1C(=O)C1=CN=CN1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 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: [22, 19, 13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 1, 1, 22, 39, 39, 55, 71, 109, 109, 109, 109, 109, 22, 22, 22, 19, 19, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 55, 55, 109] 109 rigid atoms, others: [37, 38, 39, 8, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42]) total number of confs: 319 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: REAL300025241355 none CN(CC1CCCN1C(=O)C1=CN=CN1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 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: [61, 61, 61, 75, 78, 78, 78, 78, 78, 95, 95, 109, 109, 109, 109, 34, 61, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 75, 75, 78, 78, 78, 78, 78, 78, 78, 109, 109, 109, 34, 34, 1] 109 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: 389 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: REAL300025241355 none CN(CC1CCCN1C(=O)C1=CN=CN1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 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, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 13, 7, 12, 12, 22, 32, 78, 78, 78, 78, 78, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 22, 22, 78] 109 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 198 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241355 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241355 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241355/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241355/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241355 Building REAL300025241356 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241356' /scratch/stefan/7787021/working/building/REAL300025241356 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241356 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241356/0 /scratch/stefan/7787021/working/building/REAL300025241356 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/224 `/scratch/stefan/7787021/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=N1) `REAL300025241356.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241356 none CC1=NOC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 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: [6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 7, 7, 15, 15, 39, 65, 165, 165, 165, 165, 165, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 39, 39, 165] 201 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 354 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: REAL300025241356 none CC1=NOC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 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: [201, 201, 201, 201, 181, 165, 181, 165, 165, 165, 165, 150, 110, 79, 110, 29, 79, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 165, 165, 165, 165, 165, 165, 165, 150, 150, 110, 110, 110, 29, 29, 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: 750 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: REAL300025241356 none CC1=NOC(C(=O)N2CCCC2CN(C)C(=O)CSC2=NNC(=O)[N-]2)=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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 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, 1, 1, 4, 4, 6, 6, 6, 6, 6, 13, 18, 18, 41, 41, 85, 118, 201, 201, 201, 201, 201, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 13, 13, 18, 18, 18, 85, 85, 201] 201 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: 565 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241356 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241356 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241356/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241356 Building REAL300025241357 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241357' /scratch/stefan/7787021/working/building/REAL300025241357 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241357 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241357/0 /scratch/stefan/7787021/working/building/REAL300025241357 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/225 `/scratch/stefan/7787021/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241357.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241357 none CCOC(=O)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 5, 7, 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: [201, 200, 200, 138, 200, 62, 62, 62, 62, 62, 62, 62, 58, 48, 37, 48, 16, 37, 10, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 138, 138, 62, 62, 62, 62, 62, 62, 62, 58, 58, 48, 48, 48, 16, 16, 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: 776 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241357 none CCOC(=O)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 5, 7, 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: [43, 27, 27, 9, 27, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 5, 5, 10, 10, 23, 31, 62, 62, 62, 62, 62, 43, 43, 43, 43, 43, 9, 9, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 23, 23, 62] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 320 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241357 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241357 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241357/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241357 Building REAL300025241358 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241358' /scratch/stefan/7787021/working/building/REAL300025241358 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241358 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241358/0 /scratch/stefan/7787021/working/building/REAL300025241358 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/226 `/scratch/stefan/7787021/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1CC(=O)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241358.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241358 none CN(CC1CCCN1C(=O)C1CC(=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 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: [25, 18, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 1, 1, 25, 49, 49, 85, 121, 201, 201, 201, 201, 201, 25, 25, 25, 18, 18, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 85, 85, 201] 201 rigid atoms, others: [37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44]) total number of confs: 548 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241358 none CN(CC1CCCN1C(=O)C1CC(=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 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: [95, 89, 95, 121, 122, 122, 122, 122, 122, 122, 122, 201, 201, 201, 201, 40, 89, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 121, 121, 122, 122, 122, 122, 122, 122, 122, 201, 201, 201, 201, 201, 40, 40, 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: 785 number of broken/clashed sets: 61 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241358 none CN(CC1CCCN1C(=O)C1CC(=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 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, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 19, 19, 40, 61, 122, 122, 122, 122, 122, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 40, 40, 122] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 310 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241358 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241358 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241358/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241358 Building REAL300025241359 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241359' /scratch/stefan/7787021/working/building/REAL300025241359 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241359 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241359/0 /scratch/stefan/7787021/working/building/REAL300025241359 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/227 `/scratch/stefan/7787021/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CN1C=CN=N1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241359.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241359 none CN(CC1CCCN1C(=O)CN1C=CN=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 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: [11, 11, 9, 9, 9, 9, 9, 7, 5, 7, 1, 1, 1, 1, 1, 1, 11, 12, 12, 16, 21, 29, 29, 29, 29, 29, 11, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 9, 5, 5, 1, 1, 16, 16, 29] 29 rigid atoms, others: [40, 41, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 85 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: REAL300025241359 none CN(CC1CCCN1C(=O)CN1C=CN=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 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: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 29, 29, 29, 29, 29, 21, 21, 11, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 29, 29, 29, 29, 21, 21, 1] 29 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: 114 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: REAL300025241359 none CN(CC1CCCN1C(=O)CN1C=CN=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 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: [4, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 9, 9, 9, 9, 4, 5, 5, 8, 11, 21, 21, 21, 21, 21, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 8, 8, 21] 29 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 79 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241359 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241359 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241359/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241359 Building REAL300025241360 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241360' /scratch/stefan/7787021/working/building/REAL300025241360 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300025241360 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241360/0 /scratch/stefan/7787021/working/building/REAL300025241360 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/228 `/scratch/stefan/7787021/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)[C@H]1CCCC[N@@H+]1C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241360.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241360 none CN(CC1CCCN1C(=O)[C@H]1CCCC[N@@H+]1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 9, 6, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [4, 3, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 12, 15, 23, 23, 23, 23, 23, 4, 4, 4, 3, 3, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 12, 23] 23 rigid atoms, others: [48, 45, 43, 47, 8, 41, 10, 11, 12, 13, 14, 44, 16, 17, 18, 46, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 49, 50, 51, 52, 53, 54]) total number of confs: 73 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: REAL300025241360 none CN(CC1CCCN1C(=O)[C@H]1CCCC[N@@H+]1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 9, 6, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 16, 23, 9, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 16, 16, 1] 23 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: 73 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: REAL300025241360 none CN(CC1CCCN1C(=O)[C@H]1CCCC[N@@H+]1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 9, 6, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [4, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 5, 5, 12, 15, 23, 23, 23, 23, 23, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 23] 23 rigid atoms, others: [2, 3, 4, 5, 6, 7, 40, 39, 34, 8, 35, 36, 38, 37] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 70 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241360 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241360/1 /scratch/stefan/7787021/working/building/REAL300025241360 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/229 `/scratch/stefan/7787021/working/3D/229' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)[C@H]1CCCC[N@H+]1C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241360.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241360/1/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: REAL300025241360 none CN(CC1CCCN1C(=O)[C@H]1CCCC[N@H+]1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 9, 6, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 14, 16, 21, 21, 21, 21, 21, 5, 5, 5, 4, 4, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 14, 21] 21 rigid atoms, others: [48, 45, 43, 47, 8, 41, 10, 11, 12, 13, 14, 44, 16, 17, 18, 46, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 49, 50, 51, 52, 53, 54]) total number of confs: 77 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: REAL300025241360 none CN(CC1CCCN1C(=O)[C@H]1CCCC[N@H+]1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 9, 6, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 14, 18, 9, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 14, 14, 1] 21 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: 72 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: REAL300025241360 none CN(CC1CCCN1C(=O)[C@H]1CCCC[N@H+]1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 9, 6, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 4, 5, 5, 13, 15, 21, 21, 21, 21, 21, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 21] 21 rigid atoms, others: [2, 3, 4, 5, 6, 7, 40, 39, 34, 8, 35, 36, 38, 37] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 77 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241360 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `2' /scratch/stefan/7787021/working/building/REAL300025241360/2 /scratch/stefan/7787021/working/building/REAL300025241360 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 2 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/230 `/scratch/stefan/7787021/working/3D/230' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)[C@H]1CCCCN1C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241360.mol2' -> `2.mol2' `temp.mol2' -> `REAL300025241360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241360/2/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: REAL300025241360 none CN(CC1CCCN1C(=O)[C@H]1CCCCN1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 10, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 15, 8, 8, 8, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 23, 56, 56, 96, 127, 201, 201, 201, 201, 201, 23, 23, 23, 15, 15, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 96, 96, 201] 201 rigid atoms, others: [45, 43, 17, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 48, 49, 50, 51, 52, 53]) total number of confs: 539 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241360 none CN(CC1CCCN1C(=O)[C@H]1CCCCN1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 10, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 113, 137, 169, 176, 176, 176, 176, 176, 190, 190, 201, 201, 201, 201, 201, 201, 201, 40, 113, 12, 1, 1, 1, 1, 1, 1, 1, 137, 137, 137, 169, 169, 176, 176, 176, 176, 176, 176, 176, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 40, 40, 1] 201 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: 747 number of broken/clashed sets: 60 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241360 none CN(CC1CCCN1C(=O)[C@H]1CCCCN1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 10, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 8, 10, 30, 30, 60, 88, 176, 176, 176, 176, 176, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 60, 60, 176] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 39, 34, 35, 36, 38, 37] 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 417 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241360 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241360 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241360/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241360/1.* 2: /scratch/stefan/7787021/working/building/REAL300025241360/2.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241360 Building REAL300025241361 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241361' /scratch/stefan/7787021/working/building/REAL300025241361 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241361 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241361/0 /scratch/stefan/7787021/working/building/REAL300025241361 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/231 `/scratch/stefan/7787021/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241361.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241361 none CCC(C)C(O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 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, 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, 192, 201, 117, 192, 108, 117, 108, 108, 108, 108, 104, 93, 64, 93, 27, 64, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 192, 576, 108, 108, 108, 108, 108, 108, 108, 104, 104, 93, 93, 93, 27, 27, 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: 1446 number of broken/clashed sets: 223 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241361 none CCC(C)C(O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 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, 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: [8, 8, 5, 8, 3, 5, 1, 3, 1, 1, 1, 1, 1, 1, 4, 5, 5, 11, 11, 32, 51, 108, 108, 108, 108, 108, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 15, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 32, 32, 108] 603 rigid atoms, others: [43, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 301 number of broken/clashed sets: 223 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241361 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241361 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241361/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241361 Building REAL300025241362 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241362' /scratch/stefan/7787021/working/building/REAL300025241362 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241362 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241362/0 /scratch/stefan/7787021/working/building/REAL300025241362 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/232 `/scratch/stefan/7787021/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)=C1CC1) `REAL300025241362.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241362 none CC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)=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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens need 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, 126, 141, 126, 126, 126, 126, 122, 92, 88, 92, 40, 88, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 126, 126, 126, 126, 126, 126, 126, 122, 122, 92, 92, 92, 40, 40, 1, 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]) total number of confs: 790 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: REAL300025241362 none CC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)=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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 13, 21, 21, 44, 44, 84, 119, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 13, 13, 21, 21, 21, 84, 84, 201, 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: 569 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: REAL300025241362 none CC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)=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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 1, 1, 1, 3, 7, 7, 14, 14, 30, 47, 126, 126, 126, 126, 126, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 30, 30, 126, 7, 7, 7, 7] 201 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 34, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 277 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241362 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241362 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241362/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241362 Building REAL300025241363 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241363' /scratch/stefan/7787021/working/building/REAL300025241363 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241363 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241363/0 /scratch/stefan/7787021/working/building/REAL300025241363 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/233 `/scratch/stefan/7787021/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241363.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241363 none CC1=CC1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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: [12, 12, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 8, 8, 15, 15, 27, 44, 116, 116, 116, 116, 116, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 8, 8, 27, 27, 116] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 268 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: REAL300025241363 none CC1=CC1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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: [201, 201, 201, 119, 116, 119, 116, 116, 116, 116, 114, 89, 84, 89, 36, 84, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 116, 116, 116, 116, 116, 116, 116, 114, 114, 89, 89, 89, 36, 36, 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: 759 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: REAL300025241363 none CC1=CC1C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 1, 7, 7, 12, 12, 12, 12, 12, 19, 27, 27, 50, 50, 80, 114, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 12, 12, 12, 12, 12, 12, 12, 19, 19, 27, 27, 27, 80, 80, 201] 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: 539 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241363 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241363 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241363/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241363 Building REAL300025241364 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241364' /scratch/stefan/7787021/working/building/REAL300025241364 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241364 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241364/0 /scratch/stefan/7787021/working/building/REAL300025241364 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/234 `/scratch/stefan/7787021/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241364.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241364 none CN(C)C(=O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 6, 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 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, 5, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1] 6 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: 10 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: REAL300025241364 none CN(C)C(=O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 6, 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 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, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 5] 6 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 25 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241364 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241364 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241364/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241364 Building REAL300025241365 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241365' /scratch/stefan/7787021/working/building/REAL300025241365 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241365 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241365/0 /scratch/stefan/7787021/working/building/REAL300025241365 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/235 `/scratch/stefan/7787021/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241365.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241365 none CCCC(O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 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, 181, 123, 181, 117, 123, 117, 117, 117, 117, 115, 101, 66, 101, 24, 66, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 181, 543, 117, 117, 117, 117, 117, 117, 117, 115, 115, 101, 101, 101, 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: 1346 number of broken/clashed sets: 374 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241365 none CCCC(O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 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, 7, 3, 7, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 29, 48, 117, 117, 117, 117, 117, 13, 13, 13, 13, 13, 13, 13, 7, 21, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 29, 29, 117] 603 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 325 number of broken/clashed sets: 374 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241365 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241365 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241365/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241365 Building REAL300025241366 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241366' /scratch/stefan/7787021/working/building/REAL300025241366 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241366 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241366/0 /scratch/stefan/7787021/working/building/REAL300025241366 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/236 `/scratch/stefan/7787021/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241366.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241366 none CCCCC(O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 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, 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, 200, 174, 124, 174, 118, 124, 118, 118, 118, 118, 112, 94, 65, 94, 24, 65, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 200, 200, 174, 522, 118, 118, 118, 118, 118, 118, 118, 112, 112, 94, 94, 94, 24, 24, 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: 1343 number of broken/clashed sets: 363 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241366 none CCCCC(O)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 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, 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, 13, 8, 3, 8, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 26, 46, 118, 118, 118, 118, 118, 14, 14, 14, 14, 14, 14, 14, 13, 13, 8, 24, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 26, 26, 118] 603 rigid atoms, others: [43, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 324 number of broken/clashed sets: 363 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241366 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241366 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241366/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241366 Building REAL300025241367 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241367' /scratch/stefan/7787021/working/building/REAL300025241367 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241367 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241367/0 /scratch/stefan/7787021/working/building/REAL300025241367 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/237 `/scratch/stefan/7787021/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)C(C)O) `REAL300025241367.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241367 none COC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)C(C)O 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', 'C.3', 'N.am', 'C.3', '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, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 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] 1 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: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 9, 9, 9, 9, 27] 27 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]) total number of confs: 42 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: REAL300025241367 none COC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)C(C)O 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', 'C.3', 'N.am', 'C.3', '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, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 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] 1 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 6, 7, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 9, 2, 2, 2, 2, 6] 27 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 30, 31] set([0, 1, 2, 4, 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]) total number of confs: 39 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241367 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241367 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241367/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241367 Building REAL300025241368 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241368' /scratch/stefan/7787021/working/building/REAL300025241368 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241368 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241368/0 /scratch/stefan/7787021/working/building/REAL300025241368 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/238 `/scratch/stefan/7787021/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1CC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241368.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241368 none CN(CC1CCCN1C(=O)CSC1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 16, 16, 16, 16, 16, 16, 14, 16, 4, 1, 1, 1, 1, 19, 24, 24, 33, 36, 43, 43, 43, 43, 43, 19, 19, 19, 19, 19, 16, 16, 16, 16, 16, 16, 16, 14, 14, 1, 1, 1, 1, 1, 33, 33, 43] 43 rigid atoms, others: [43, 39, 40, 41, 42, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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]) total number of confs: 151 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: REAL300025241368 none CN(CC1CCCN1C(=O)CSC1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 16, 16, 25, 38, 43, 43, 15, 15, 10, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 25, 25, 43, 43, 43, 43, 43, 15, 15, 1] 43 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: 137 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: REAL300025241368 none CN(CC1CCCN1C(=O)CSC1CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 12, 16, 16, 3, 4, 4, 7, 9, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 16, 16, 16, 7, 7, 15] 43 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 78 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241368 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241368 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241368/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241368 Building REAL300025241369 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241369' /scratch/stefan/7787021/working/building/REAL300025241369 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241369 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241369/0 /scratch/stefan/7787021/working/building/REAL300025241369 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/239 `/scratch/stefan/7787021/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CCCC1CCC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241369.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241369 none CN(CC1CCCN1C(=O)CCCC1CCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 18, 18, 10, 18, 7, 5, 1, 1, 1, 1, 1, 30, 36, 36, 71, 104, 201, 201, 201, 201, 201, 30, 30, 30, 30, 30, 18, 18, 18, 18, 18, 18, 18, 10, 10, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 71, 71, 201] 201 rigid atoms, others: [48, 45, 12, 13, 14, 15, 16, 49, 50, 51, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 52, 53, 54]) total number of confs: 593 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241369 none CN(CC1CCCN1C(=O)CCCC1CCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 38, 52, 52, 52, 52, 52, 52, 52, 52, 107, 118, 122, 201, 201, 201, 21, 30, 13, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 52, 52, 52, 52, 52, 52, 52, 52, 52, 107, 107, 119, 119, 122, 122, 201, 201, 201, 201, 201, 201, 201, 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: 860 number of broken/clashed sets: 146 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241369 none CN(CC1CCCN1C(=O)CCCC1CCC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 7, 10, 18, 18, 18, 3, 4, 4, 9, 14, 52, 52, 52, 52, 52, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 10, 10, 18, 18, 18, 18, 18, 18, 18, 9, 9, 52] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 175 number of broken/clashed sets: 146 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241369 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241369 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241369/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241369 Building REAL300025241370 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241370' /scratch/stefan/7787021/working/building/REAL300025241370 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241370 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241370/0 /scratch/stefan/7787021/working/building/REAL300025241370 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/240 `/scratch/stefan/7787021/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(O)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241370.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241370 none CCC(O)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 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] 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, 201, 142, 142, 142, 142, 142, 142, 142, 135, 108, 76, 108, 27, 76, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 603, 185, 185, 142, 142, 142, 142, 142, 142, 142, 135, 135, 108, 108, 108, 27, 27, 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: 1456 number of broken/clashed sets: 261 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241370 none CCC(O)CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 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] 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, 10, 8, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 5, 5, 11, 11, 33, 57, 142, 142, 142, 142, 142, 12, 12, 12, 12, 12, 10, 30, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 33, 33, 142] 603 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 374 number of broken/clashed sets: 261 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241370 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241370 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241370/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241370 Building REAL300025241371 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241371' /scratch/stefan/7787021/working/building/REAL300025241371 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241371 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241371/0 /scratch/stefan/7787021/working/building/REAL300025241371 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/241 `/scratch/stefan/7787021/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1CCC(=O)N1C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241371.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241371 none CN(CC1CCCN1C(=O)C1CCC(=O)N1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 26, 55, 55, 98, 134, 201, 201, 201, 201, 201, 26, 26, 26, 17, 17, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 2, 2, 2, 98, 98, 201] 201 rigid atoms, others: [43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 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]) total number of confs: 565 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241371 none CN(CC1CCCN1C(=O)C1CCC(=O)N1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 105, 126, 162, 166, 166, 166, 166, 166, 181, 181, 201, 201, 201, 201, 201, 201, 40, 105, 13, 1, 1, 1, 1, 1, 1, 1, 126, 126, 126, 162, 162, 166, 166, 166, 166, 166, 166, 166, 201, 201, 201, 201, 201, 201, 201, 201, 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: 770 number of broken/clashed sets: 63 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241371 none CN(CC1CCCN1C(=O)C1CCC(=O)N1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 10, 28, 28, 58, 92, 166, 166, 166, 166, 166, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 58, 58, 166] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 410 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241371 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241371 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241371/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241371 Building REAL300025241372 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241372' /scratch/stefan/7787021/working/building/REAL300025241372 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241372 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241372/0 /scratch/stefan/7787021/working/building/REAL300025241372 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/242 `/scratch/stefan/7787021/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=NNC=C1C#N)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241372.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241372 none CN(CC1CCCN1C(=O)C1=NNC=C1C#N)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [26, 20, 12, 12, 12, 12, 12, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 26, 46, 46, 72, 101, 160, 160, 160, 160, 160, 26, 26, 26, 20, 20, 12, 12, 12, 12, 12, 12, 12, 1, 1, 72, 72, 160] 160 rigid atoms, others: [39, 8, 10, 11, 12, 13, 14, 15, 16, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 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]) total number of confs: 439 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: REAL300025241372 none CN(CC1CCCN1C(=O)C1=NNC=C1C#N)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [94, 88, 94, 124, 127, 127, 127, 127, 127, 145, 145, 160, 160, 160, 160, 160, 160, 36, 88, 13, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 124, 124, 127, 127, 127, 127, 127, 127, 127, 160, 160, 36, 36, 1] 160 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: 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: REAL300025241372 none CN(CC1CCCN1C(=O)C1=NNC=C1C#N)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 12, 12, 12, 12, 12, 10, 17, 17, 33, 55, 127, 127, 127, 127, 127, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 33, 33, 127] 160 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43]) total number of confs: 292 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241372 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241372 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241372/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241372 Building REAL300025241373 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241373' /scratch/stefan/7787021/working/building/REAL300025241373 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241373 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241373/0 /scratch/stefan/7787021/working/building/REAL300025241373 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/243 `/scratch/stefan/7787021/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241373.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241373 none CNC(=O)CCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 7, 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 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, 195, 130, 129, 130, 129, 129, 129, 129, 127, 89, 67, 89, 27, 67, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 197, 197, 195, 195, 129, 129, 129, 129, 129, 129, 129, 127, 127, 89, 89, 89, 27, 27, 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: 876 number of broken/clashed sets: 132 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241373 none CNC(=O)CCC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 7, 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 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, 18, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 6, 6, 9, 9, 19, 35, 129, 129, 129, 129, 129, 18, 18, 18, 18, 10, 10, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 19, 19, 129] 201 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 282 number of broken/clashed sets: 132 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241373 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241373 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241373/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241373 Building REAL300025241374 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241374' /scratch/stefan/7787021/working/building/REAL300025241374 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241374 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241374/0 /scratch/stefan/7787021/working/building/REAL300025241374 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/244 `/scratch/stefan/7787021/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CCC1=CON=C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241374.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241374 none CN(CC1CCCN1C(=O)CCC1=CON=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 12, 8, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 16, 16, 16, 16, 16, 15, 7, 15, 3, 1, 1, 1, 1, 1, 1, 18, 21, 21, 29, 31, 38, 38, 38, 38, 38, 18, 18, 18, 18, 18, 16, 16, 16, 16, 16, 16, 16, 7, 7, 3, 3, 1, 1, 29, 29, 38] 38 rigid atoms, others: [11, 44, 43, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 132 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: REAL300025241374 none CN(CC1CCCN1C(=O)CCC1=CON=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 12, 8, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 22, 22, 38, 38, 38, 38, 13, 13, 9, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 22, 22, 22, 22, 38, 38, 13, 13, 1] 38 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: 108 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: REAL300025241374 none CN(CC1CCCN1C(=O)CCC1=CON=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 12, 8, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 16, 16, 16, 16, 3, 4, 4, 7, 9, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 16, 16, 7, 7, 13] 38 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 79 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241374 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241374 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241374/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241374 Building REAL300025241375 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241375' /scratch/stefan/7787021/working/building/REAL300025241375 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241375 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241375/0 /scratch/stefan/7787021/working/building/REAL300025241375 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/245 `/scratch/stefan/7787021/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC1=CSN=C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241375.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241375 none CN(CC1CCCN1C(=O)CC1=CSN=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 14, 8, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 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: [21, 21, 18, 18, 18, 18, 18, 14, 5, 14, 1, 1, 1, 1, 1, 1, 21, 25, 25, 35, 35, 44, 44, 44, 44, 44, 21, 21, 21, 21, 21, 18, 18, 18, 18, 18, 18, 18, 5, 5, 1, 1, 35, 35, 44] 44 rigid atoms, others: [40, 41, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 143 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: REAL300025241375 none CN(CC1CCCN1C(=O)CC1=CSN=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 14, 8, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 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: [17, 17, 17, 17, 17, 17, 17, 17, 17, 18, 18, 31, 44, 44, 44, 44, 16, 17, 11, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 31, 31, 44, 44, 16, 16, 1] 44 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: 136 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: REAL300025241375 none CN(CC1CCCN1C(=O)CC1=CSN=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 14, 8, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 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: [4, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 18, 18, 18, 18, 4, 5, 5, 8, 10, 17, 17, 17, 17, 17, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 18, 18, 8, 8, 17] 44 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 94 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241375 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241375 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241375/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241375 Building REAL300025241376 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241376' /scratch/stefan/7787021/working/building/REAL300025241376 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241376 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241376/0 /scratch/stefan/7787021/working/building/REAL300025241376 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/246 `/scratch/stefan/7787021/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)[NH+](C)C) `REAL300025241376.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241376 none C=CCC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)[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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 27, 23, 23, 23, 23, 23, 23, 23, 22, 19, 14, 19, 7, 14, 6, 1, 1, 1, 1, 1, 1, 1, 27, 29, 29, 29, 48, 48, 48, 48, 48, 27, 23, 23, 23, 23, 23, 23, 23, 22, 22, 19, 19, 19, 7, 7, 1, 29, 29, 29, 29, 29, 29] 48 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: 227 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: REAL300025241376 none C=CCC(C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1)[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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 5, 5, 8, 8, 13, 15, 23, 23, 23, 23, 23, 5, 6, 6, 6, 15, 15, 15, 10, 10, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 13, 13, 23, 6, 6, 6, 6, 6, 6] 48 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 39, 11, 40, 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, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 130 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241376 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241376 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241376/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241376 Building REAL300025241377 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241377' /scratch/stefan/7787021/working/building/REAL300025241377 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241377 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241377/0 /scratch/stefan/7787021/working/building/REAL300025241377 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/247 `/scratch/stefan/7787021/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CCCCF)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241377.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241377 none CN(CC1CCCN1C(=O)CCCCF)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 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: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 24, 30, 30, 30, 10, 10, 8, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 24, 24, 30, 30, 30, 30, 30, 30, 10, 10, 1] 30 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: 114 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: REAL300025241377 none CN(CC1CCCN1C(=O)CCCCF)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 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: [2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 9, 9, 11, 2, 3, 3, 6, 8, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 9, 9, 11, 11, 6, 6, 10] 30 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 76 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241377 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241377 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241377/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241377 Building REAL300025241378 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241378' /scratch/stefan/7787021/working/building/REAL300025241378 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241378 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241378/0 /scratch/stefan/7787021/working/building/REAL300025241378 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/248 `/scratch/stefan/7787021/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CC(=O)C=CN1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241378.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241378 none CN(CC1CCCN1C(=O)C1=CC(=O)C=CN1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 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] 0 hydrogens 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, 16, 16, 16, 16, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 30, 54, 54, 91, 124, 201, 201, 201, 201, 201, 30, 30, 30, 26, 26, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 91, 91, 201] 201 rigid atoms, others: [39, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 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]) total number of confs: 571 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: REAL300025241378 none CN(CC1CCCN1C(=O)C1=CC(=O)C=CN1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 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] 0 hydrogens 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, 85, 86, 114, 117, 117, 117, 117, 117, 146, 146, 201, 201, 201, 201, 201, 201, 37, 85, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 114, 114, 117, 117, 117, 117, 117, 117, 117, 201, 201, 201, 201, 37, 37, 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: 661 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: REAL300025241378 none CN(CC1CCCN1C(=O)C1=CC(=O)C=CN1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 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] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 16, 16, 16, 16, 8, 14, 14, 28, 48, 117, 117, 117, 117, 117, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 28, 28, 117] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 274 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241378 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241378 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241378/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241378 Building REAL300025241379 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241379' /scratch/stefan/7787021/working/building/REAL300025241379 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241379 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241379/0 /scratch/stefan/7787021/working/building/REAL300025241379 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/249 `/scratch/stefan/7787021/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CC([O-])=CS1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241379.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241379 none CN(CC1CCCN1C(=O)C1=CC([O-])=CS1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'S.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 12, 1, 14, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 6, 7, 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: [31, 27, 15, 15, 15, 15, 15, 9, 1, 9, 1, 1, 1, 1, 1, 1, 31, 57, 57, 80, 124, 201, 201, 201, 201, 201, 31, 31, 31, 27, 27, 15, 15, 15, 15, 15, 15, 15, 1, 1, 80, 80, 201] 201 rigid atoms, others: [38, 39, 8, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 536 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: REAL300025241379 none CN(CC1CCCN1C(=O)C1=CC([O-])=CS1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'S.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 12, 1, 14, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 6, 7, 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: [93, 84, 93, 112, 116, 116, 116, 116, 116, 147, 147, 201, 201, 201, 201, 201, 33, 84, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 112, 112, 116, 116, 116, 116, 116, 116, 116, 201, 201, 33, 33, 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: 624 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: REAL300025241379 none CN(CC1CCCN1C(=O)C1=CC([O-])=CS1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'S.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 12, 1, 14, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 6, 7, 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: [6, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 15, 15, 6, 11, 11, 18, 32, 116, 116, 116, 116, 116, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 18, 18, 116] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42]) total number of confs: 227 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241379 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241379 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241379/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241379 Building REAL300025241380 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241380' /scratch/stefan/7787021/working/building/REAL300025241380 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241380 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241380/0 /scratch/stefan/7787021/working/building/REAL300025241380 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/250 `/scratch/stefan/7787021/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CSN=C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241380.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241380 none CN(CC1CCCN1C(=O)C1=CSN=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 14, 8, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 21, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 1, 1, 29, 47, 47, 75, 111, 201, 201, 201, 201, 201, 29, 29, 29, 21, 21, 12, 12, 12, 12, 12, 12, 12, 1, 1, 75, 75, 201] 201 rigid atoms, others: [37, 38, 8, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 533 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: REAL300025241380 none CN(CC1CCCN1C(=O)C1=CSN=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 14, 8, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 80, 85, 111, 115, 115, 115, 115, 115, 133, 133, 201, 201, 201, 201, 37, 80, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 111, 111, 115, 115, 115, 115, 115, 115, 115, 201, 201, 37, 37, 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: 648 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: REAL300025241380 none CN(CC1CCCN1C(=O)C1=CSN=C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 14, 8, 1, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 12, 12, 12, 7, 12, 12, 23, 40, 115, 115, 115, 115, 115, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 23, 23, 115] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 249 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241380 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241380 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241380/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241380 Building REAL300025241381 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241381' /scratch/stefan/7787021/working/building/REAL300025241381 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241381 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241381/0 /scratch/stefan/7787021/working/building/REAL300025241381 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/251 `/scratch/stefan/7787021/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CC(N)=NN1C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241381.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241381 none CN(CC1CCCN1C(=O)C1=CC(N)=NN1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [30, 23, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 30, 52, 52, 94, 131, 201, 201, 201, 201, 201, 30, 30, 30, 23, 23, 12, 12, 12, 12, 12, 12, 12, 1, 2, 2, 2, 2, 2, 94, 94, 201] 201 rigid atoms, others: [39, 8, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 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]) total number of confs: 578 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: REAL300025241381 none CN(CC1CCCN1C(=O)C1=CC(N)=NN1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [87, 82, 87, 122, 129, 129, 129, 129, 129, 172, 172, 201, 201, 201, 201, 201, 201, 38, 82, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 122, 122, 129, 129, 129, 129, 129, 129, 129, 201, 201, 201, 201, 201, 201, 38, 38, 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: 746 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: REAL300025241381 none CN(CC1CCCN1C(=O)C1=CC(N)=NN1C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [7, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 12, 12, 12, 12, 12, 7, 12, 12, 29, 46, 129, 129, 129, 129, 129, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 29, 29, 129] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 281 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241381 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241381 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241381/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241381 Building REAL300025241382 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241382' /scratch/stefan/7787021/working/building/REAL300025241382 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241382 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241382/0 /scratch/stefan/7787021/working/building/REAL300025241382 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/252 `/scratch/stefan/7787021/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1CCC(=O)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241382.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241382 none CN(CC1CCCN1C(=O)C1CCC(=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 10, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 26, 51, 51, 93, 127, 201, 201, 201, 201, 201, 26, 26, 26, 19, 19, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 93, 93, 201] 201 rigid atoms, others: [43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47]) total number of confs: 560 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: REAL300025241382 none CN(CC1CCCN1C(=O)C1CCC(=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 92, 100, 126, 135, 135, 135, 135, 135, 140, 140, 201, 201, 201, 201, 201, 39, 92, 13, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 126, 126, 135, 135, 135, 135, 135, 135, 135, 201, 201, 201, 201, 201, 201, 201, 39, 39, 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: 780 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: REAL300025241382 none CN(CC1CCCN1C(=O)C1CCC(=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 4, 10, 10, 10, 10, 10, 9, 21, 21, 43, 61, 135, 135, 135, 135, 135, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 43, 43, 135] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 339 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241382 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241382 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241382/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241382 Building REAL300025241383 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241383' /scratch/stefan/7787021/working/building/REAL300025241383 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241383 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241383/0 /scratch/stefan/7787021/working/building/REAL300025241383 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/253 `/scratch/stefan/7787021/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1CCCSC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241383.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241383 none CN(CC1CCCN1C(=O)C1CCCSC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 23, 45, 45, 86, 120, 201, 201, 201, 201, 201, 23, 23, 23, 14, 14, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 86, 86, 201] 201 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 529 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241383 none CN(CC1CCCN1C(=O)C1CCCSC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 84, 95, 123, 124, 124, 124, 124, 124, 129, 129, 201, 201, 201, 201, 201, 37, 84, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 123, 123, 124, 124, 124, 124, 124, 124, 124, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 794 number of broken/clashed sets: 70 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241383 none CN(CC1CCCN1C(=O)C1CCCSC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7] 0 hydrogens 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, 1, 4, 4, 8, 8, 8, 8, 8, 9, 18, 18, 39, 57, 124, 124, 124, 124, 124, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 39, 39, 124] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 301 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241383 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241383 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241383/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241383 Building REAL300025241384 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241384' /scratch/stefan/7787021/working/building/REAL300025241384 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241384 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241384/0 /scratch/stefan/7787021/working/building/REAL300025241384 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/254 `/scratch/stefan/7787021/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)[C@H]1CC(=O)N1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241384.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241384 none CN(CC1CCCN1C(=O)[C@H]1CC(=O)N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 19, 12, 12, 12, 12, 12, 6, 1, 6, 1, 1, 1, 1, 1, 1, 26, 49, 49, 91, 126, 201, 201, 201, 201, 201, 26, 26, 26, 19, 19, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 91, 91, 201] 201 rigid atoms, others: [38, 39, 8, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43]) total number of confs: 576 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241384 none CN(CC1CCCN1C(=O)[C@H]1CC(=O)N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 84, 86, 121, 126, 126, 126, 126, 126, 128, 128, 201, 201, 201, 201, 201, 35, 84, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 121, 121, 126, 126, 126, 126, 126, 126, 126, 201, 201, 201, 35, 35, 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: 802 number of broken/clashed sets: 64 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241384 none CN(CC1CCCN1C(=O)[C@H]1CC(=O)N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 1, 4, 4, 12, 12, 12, 12, 12, 9, 17, 17, 39, 59, 126, 126, 126, 126, 126, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 39, 39, 126] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43]) total number of confs: 327 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241384 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241384 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241384/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241384 Building REAL300025241385 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241385' /scratch/stefan/7787021/working/building/REAL300025241385 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241385 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241385/0 /scratch/stefan/7787021/working/building/REAL300025241385 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/255 `/scratch/stefan/7787021/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=NN(C)C=C1N)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241385.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241385 none CN(CC1CCCN1C(=O)C1=NN(C)C=C1N)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 5, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 30, 62, 62, 91, 126, 201, 201, 201, 201, 201, 30, 30, 30, 23, 23, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 91, 91, 201] 201 rigid atoms, others: [43, 8, 44, 10, 11, 12, 13, 14, 15, 16, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47]) total number of confs: 564 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: REAL300025241385 none CN(CC1CCCN1C(=O)C1=NN(C)C=C1N)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 5, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 96, 108, 138, 141, 141, 141, 141, 141, 177, 177, 201, 201, 201, 201, 201, 201, 39, 96, 13, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 138, 138, 141, 141, 141, 141, 141, 141, 141, 201, 201, 201, 201, 201, 201, 39, 39, 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: 709 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: REAL300025241385 none CN(CC1CCCN1C(=O)C1=NN(C)C=C1N)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 5, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 13, 13, 13, 7, 12, 12, 24, 45, 141, 141, 141, 141, 141, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 24, 24, 141] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 282 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241385 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241385 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241385/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241385 Building REAL300025241386 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241386' /scratch/stefan/7787021/working/building/REAL300025241386 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241386 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241386/0 /scratch/stefan/7787021/working/building/REAL300025241386 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/256 `/scratch/stefan/7787021/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C=C(C#N)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241386.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241386 none CC(C)C=C(C#N)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 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 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, 201, 201, 130, 136, 130, 130, 130, 130, 122, 103, 76, 103, 28, 76, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 130, 130, 130, 130, 130, 130, 130, 122, 122, 103, 103, 103, 28, 28, 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: 738 number of broken/clashed sets: 107 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241386 none CC(C)C=C(C#N)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 7, 14, 7, 3, 7, 7, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 22, 36, 130, 130, 130, 130, 130, 14, 14, 14, 14, 14, 14, 14, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 22, 22, 130] 201 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 280 number of broken/clashed sets: 107 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241386 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241386 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241386/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241386 Building REAL300025241387 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241387' /scratch/stefan/7787021/working/building/REAL300025241387 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241387 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241387/0 /scratch/stefan/7787021/working/building/REAL300025241387 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/257 `/scratch/stefan/7787021/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=NSC=C1N)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241387.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241387 none CN(CC1CCCN1C(=O)C1=NSC=C1N)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 14, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 18, 10, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 26, 55, 55, 82, 125, 201, 201, 201, 201, 201, 26, 26, 26, 18, 18, 10, 10, 10, 10, 10, 10, 10, 1, 2, 2, 82, 82, 201] 201 rigid atoms, others: [38, 8, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43]) total number of confs: 542 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: REAL300025241387 none CN(CC1CCCN1C(=O)C1=NSC=C1N)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 14, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 93, 104, 134, 139, 139, 139, 139, 139, 183, 183, 201, 201, 201, 201, 201, 38, 93, 13, 1, 1, 1, 1, 1, 1, 1, 104, 104, 104, 134, 134, 139, 139, 139, 139, 139, 139, 139, 201, 201, 201, 38, 38, 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: 709 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: REAL300025241387 none CN(CC1CCCN1C(=O)C1=NSC=C1N)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 14, 1, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 10, 9, 16, 16, 30, 52, 139, 139, 139, 139, 139, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 30, 30, 139] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43]) total number of confs: 297 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241387 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241387 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241387/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241387 Building REAL300025241388 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241388' /scratch/stefan/7787021/working/building/REAL300025241388 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241388 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241388/0 /scratch/stefan/7787021/working/building/REAL300025241388 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/258 `/scratch/stefan/7787021/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CN1C=NC=N1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241388.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241388 none CN(CC1CCCN1C(=O)CN1C=NC=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 12, 12, 12, 12, 12, 10, 6, 10, 1, 1, 1, 1, 1, 1, 15, 19, 19, 24, 27, 31, 31, 31, 31, 31, 15, 15, 15, 15, 15, 12, 12, 12, 12, 12, 12, 12, 6, 6, 1, 1, 24, 24, 31] 31 rigid atoms, others: [40, 41, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 108 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: REAL300025241388 none CN(CC1CCCN1C(=O)CN1C=NC=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 30, 31, 31, 31, 31, 19, 20, 10, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 30, 30, 31, 31, 19, 19, 1] 31 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: 125 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: REAL300025241388 none CN(CC1CCCN1C(=O)CN1C=NC=N1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 12, 12, 12, 12, 4, 6, 6, 10, 13, 20, 20, 20, 20, 20, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 12, 12, 10, 10, 20] 31 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 92 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241388 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241388 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241388/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241388 Building REAL300025241389 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241389' /scratch/stefan/7787021/working/building/REAL300025241389 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241389 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241389/0 /scratch/stefan/7787021/working/building/REAL300025241389 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/259 `/scratch/stefan/7787021/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)OC)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241389.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241389 none CCC(C(=O)OC)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 5, 3, 7, 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: [198, 197, 135, 197, 201, 201, 201, 135, 135, 135, 135, 135, 135, 130, 115, 76, 115, 29, 76, 13, 1, 1, 1, 1, 1, 1, 1, 198, 198, 198, 198, 198, 197, 201, 201, 201, 135, 135, 135, 135, 135, 135, 135, 130, 130, 115, 115, 115, 29, 29, 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: 773 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: REAL300025241389 none CCC(C(=O)OC)C(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 5, 3, 7, 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: [8, 6, 3, 6, 9, 9, 9, 1, 3, 1, 1, 1, 1, 1, 1, 4, 5, 5, 12, 12, 31, 51, 135, 135, 135, 135, 135, 8, 8, 8, 8, 8, 6, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 31, 31, 135] 201 rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 317 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241389 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241389 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241389/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241389 Building REAL300025241390 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241390' /scratch/stefan/7787021/working/building/REAL300025241390 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241390 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241390/0 /scratch/stefan/7787021/working/building/REAL300025241390 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/260 `/scratch/stefan/7787021/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1CSC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241390.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241390 none CN(CC1CCCN1C(=O)C1CSC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 1, 24, 40, 40, 77, 117, 201, 201, 201, 201, 201, 24, 24, 24, 16, 16, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 77, 77, 201] 201 rigid atoms, others: [36, 37, 38, 39, 8, 10, 11, 12, 13, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 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]) total number of confs: 532 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241390 none CN(CC1CCCN1C(=O)C1CSC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 88, 95, 122, 123, 123, 123, 123, 123, 125, 125, 201, 201, 201, 38, 88, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 122, 122, 123, 123, 123, 123, 123, 123, 123, 201, 201, 201, 201, 201, 38, 38, 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: 780 number of broken/clashed sets: 61 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241390 none CN(CC1CCCN1C(=O)C1CSC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 10, 17, 17, 34, 55, 123, 123, 123, 123, 123, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 34, 34, 123] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 295 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241390 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241390 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241390/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241390 Building REAL300025241391 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241391' /scratch/stefan/7787021/working/building/REAL300025241391 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241391 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241391/0 /scratch/stefan/7787021/working/building/REAL300025241391 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/261 `/scratch/stefan/7787021/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1=CN=C(N)O1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241391.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241391 none CN(CC1CCCN1C(=O)C1=CN=C(N)O1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 3, 7, 6, 7, 7, 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: [35, 23, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 35, 66, 66, 84, 125, 201, 201, 201, 201, 201, 35, 35, 35, 23, 23, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 84, 84, 201] 201 rigid atoms, others: [38, 39, 8, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43]) total number of confs: 532 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: REAL300025241391 none CN(CC1CCCN1C(=O)C1=CN=C(N)O1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 3, 7, 6, 7, 7, 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: [98, 84, 98, 146, 154, 154, 154, 154, 154, 190, 190, 201, 201, 201, 201, 201, 43, 84, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 146, 146, 154, 154, 154, 154, 154, 154, 154, 201, 201, 201, 43, 43, 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: 788 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: REAL300025241391 none CN(CC1CCCN1C(=O)C1=CN=C(N)O1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 3, 7, 6, 7, 7, 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, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 12, 12, 12, 12, 10, 18, 18, 26, 48, 154, 154, 154, 154, 154, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 26, 26, 154] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43]) total number of confs: 294 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241391 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241391 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241391/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241391 Building REAL300025241392 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241392' /scratch/stefan/7787021/working/building/REAL300025241392 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241392 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241392/0 /scratch/stefan/7787021/working/building/REAL300025241392 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/262 `/scratch/stefan/7787021/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC1(CO)CC1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241392.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241392 none CN(CC1CCCN1C(=O)CC1(CO)CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 4, 9, 1, 1, 1, 7, 1, 1, 9, 10, 10, 16, 17, 18, 18, 18, 18, 18, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 7, 7, 21, 1, 1, 1, 1, 16, 16, 18] 54 rigid atoms, others: [11, 44, 10, 43, 12, 45, 14, 15, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49]) total number of confs: 104 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: REAL300025241392 none CN(CC1CCCN1C(=O)CC1(CO)CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 17, 18, 18, 18, 18, 10, 10, 8, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 17, 17, 18, 18, 54, 18, 18, 18, 18, 10, 10, 1] 54 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: 115 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: REAL300025241392 none CN(CC1CCCN1C(=O)CC1(CO)CC1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 9, 10, 9, 9, 2, 3, 3, 6, 7, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 30, 9, 9, 9, 9, 6, 6, 10] 54 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 97 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241392 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241392 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241392/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241392 Building REAL300025241393 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241393' /scratch/stefan/7787021/working/building/REAL300025241393 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241393 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241393/0 /scratch/stefan/7787021/working/building/REAL300025241393 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/263 `/scratch/stefan/7787021/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CC1=NC=CS1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241393.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241393 none CN(CC1CCCN1C(=O)CC1=NC=CS1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 1, 14, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 4, 6, 6, 10, 12, 16, 16, 16, 16, 16, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 2, 2, 1, 1, 10, 10, 16] 16 rigid atoms, others: [40, 41, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 55 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: REAL300025241393 none CN(CC1CCCN1C(=O)CC1=NC=CS1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 1, 14, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 16, 16, 16, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 16, 16, 11, 11, 1] 16 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: 57 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: REAL300025241393 none CN(CC1CCCN1C(=O)CC1=NC=CS1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 1, 14, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 4, 4, 7, 9, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 7, 11] 16 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 44 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241393 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241393 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241393/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241393 Building REAL300025241394 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241394' /scratch/stefan/7787021/working/building/REAL300025241394 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241394 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241394/0 /scratch/stefan/7787021/working/building/REAL300025241394 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/264 `/scratch/stefan/7787021/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)C1CCC=CO1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241394.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241394 none CN(CC1CCCN1C(=O)C1CCC=CO1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 24, 48, 48, 89, 127, 201, 201, 201, 201, 201, 24, 24, 24, 17, 17, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 89, 89, 201] 201 rigid atoms, others: [43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47]) total number of confs: 563 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: REAL300025241394 none CN(CC1CCCN1C(=O)C1CCC=CO1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 103, 114, 151, 159, 159, 159, 159, 159, 174, 174, 201, 201, 201, 201, 201, 42, 103, 13, 1, 1, 1, 1, 1, 1, 1, 114, 114, 114, 151, 151, 159, 159, 159, 159, 159, 159, 159, 201, 201, 201, 201, 201, 201, 201, 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: 779 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: REAL300025241394 none CN(CC1CCCN1C(=O)C1CCC=CO1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', '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.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 12, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 8, 8, 15, 15, 34, 60, 159, 159, 159, 159, 159, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 34, 34, 159] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 340 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241394 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241394 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241394/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241394 Building REAL300025241395 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241395' /scratch/stefan/7787021/working/building/REAL300025241395 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241395 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241395/0 /scratch/stefan/7787021/working/building/REAL300025241395 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/265 `/scratch/stefan/7787021/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241395.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241395 none C=CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 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] 0 hydrogens need 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, 201, 188, 188, 188, 188, 184, 133, 113, 133, 41, 113, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 188, 188, 188, 188, 188, 188, 188, 184, 184, 133, 133, 133, 41, 41, 1] 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]) total number of confs: 757 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: REAL300025241395 none C=CC(=O)N1CCCC1CN(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 1, 1, 1, 4, 10, 10, 20, 20, 46, 84, 188, 188, 188, 188, 188, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 46, 46, 188] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 433 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241395 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241395 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241395/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241395 Building REAL300025241396 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241396' /scratch/stefan/7787021/working/building/REAL300025241396 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241396 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241396/0 /scratch/stefan/7787021/working/building/REAL300025241396 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/266 `/scratch/stefan/7787021/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CSC(N)=[NH2+]) `REAL300025241396.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241396 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CSC(N)=[NH2+] NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'S.3', 'C.cat', 'N.pl3', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 14, 1, 8, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 4, 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: [134, 123, 116, 116, 116, 116, 116, 97, 35, 97, 13, 1, 1, 1, 1, 1, 1, 1, 134, 193, 193, 199, 201, 201, 201, 201, 201, 134, 134, 134, 123, 123, 116, 116, 116, 116, 116, 116, 116, 35, 35, 1, 199, 199, 201, 201] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 648 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: REAL300025241396 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CSC(N)=[NH2+] NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'S.3', 'C.cat', 'N.pl3', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 14, 1, 8, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 4, 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, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 34, 116, 116, 116, 116, 116, 8, 12, 12, 18, 19, 19, 19, 19, 19, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 116, 18, 18, 19, 19] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 260 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241396 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241396 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241396/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241396 Building REAL300025241397 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241397' /scratch/stefan/7787021/working/building/REAL300025241397 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241397 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241397/0 /scratch/stefan/7787021/working/building/REAL300025241397 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/267 `/scratch/stefan/7787021/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CCC[N+](=O)[O-]) `REAL300025241397.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241397 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CCC[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 74, 57, 57, 57, 57, 57, 57, 25, 57, 13, 1, 1, 1, 1, 1, 1, 1, 99, 141, 141, 141, 150, 201, 201, 201, 99, 99, 99, 74, 74, 57, 57, 57, 57, 57, 57, 57, 25, 25, 1, 141, 141, 150, 150, 201, 201] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 823 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: REAL300025241397 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CCC[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 20, 57, 57, 57, 57, 57, 5, 11, 11, 11, 13, 22, 31, 31, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 57, 11, 11, 13, 13, 22, 22] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241397 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241397 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241397/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241397 Building REAL300025241398 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241398' /scratch/stefan/7787021/working/building/REAL300025241398 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241398 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241398/0 /scratch/stefan/7787021/working/building/REAL300025241398 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/268 `/scratch/stefan/7787021/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CF)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241398.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241398 none CC(CF)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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: [201, 168, 201, 201, 148, 168, 115, 148, 66, 66, 66, 66, 66, 61, 36, 61, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 148, 148, 148, 115, 115, 66, 66, 66, 66, 66, 66, 66, 36, 36, 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: 869 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: REAL300025241398 none CC(CF)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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: [26, 14, 26, 46, 9, 14, 4, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 13, 66, 66, 66, 66, 66, 26, 26, 26, 26, 46, 46, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 66] 201 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44]) total number of confs: 297 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241398 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241398 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241398/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241398 Building REAL300025241399 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241399' /scratch/stefan/7787021/working/building/REAL300025241399 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241399 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241399/0 /scratch/stefan/7787021/working/building/REAL300025241399 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/269 `/scratch/stefan/7787021/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C[C@@H]1COC[C@H]1O) `REAL300025241399.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241399 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C[C@@H]1COC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 7, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [151, 105, 74, 74, 74, 74, 74, 66, 31, 66, 13, 1, 1, 1, 1, 1, 1, 1, 151, 179, 179, 190, 201, 201, 201, 201, 201, 201, 201, 151, 151, 151, 105, 105, 74, 74, 74, 74, 74, 74, 74, 31, 31, 1, 190, 190, 201, 201, 201, 201, 603] 603 rigid atoms, others: [43, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 1378 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: REAL300025241399 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C[C@@H]1COC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 7, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 18, 25, 34, 34, 34, 34, 34, 35, 35, 71, 115, 201, 201, 201, 201, 201, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 25, 25, 34, 34, 34, 34, 34, 34, 34, 71, 71, 201, 5, 5, 1, 1, 1, 1, 3] 603 rigid atoms, others: [46, 47, 48, 49, 20, 21, 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, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50]) total number of confs: 534 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: REAL300025241399 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C[C@@H]1COC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 7, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 23, 74, 74, 74, 74, 74, 10, 17, 17, 27, 34, 34, 34, 34, 34, 34, 34, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 74, 27, 27, 34, 34, 34, 34, 102] 603 rigid atoms, others: [2, 3, 4, 5, 6, 7, 40, 39, 34, 8, 35, 36, 38, 37] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 348 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241399 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241399 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241399/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241399 Building REAL300025241400 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241400' /scratch/stefan/7787021/working/building/REAL300025241400 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241400 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241400/0 /scratch/stefan/7787021/working/building/REAL300025241400 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/270 `/scratch/stefan/7787021/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C=CC1=NC=CO1) `REAL300025241400.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241400 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C=CC1=NC=CO1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 38, 26, 26, 26, 26, 26, 26, 18, 26, 12, 1, 1, 1, 1, 1, 1, 1, 55, 101, 101, 124, 124, 201, 201, 201, 201, 55, 55, 55, 38, 38, 26, 26, 26, 26, 26, 26, 26, 18, 18, 1, 124, 124, 201, 201] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 592 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: REAL300025241400 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C=CC1=NC=CO1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 21, 30, 34, 34, 34, 34, 34, 34, 34, 57, 93, 201, 201, 201, 201, 201, 2, 11, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 30, 30, 34, 34, 34, 34, 34, 34, 34, 57, 57, 201, 2, 2, 1, 1] 201 rigid atoms, others: [44, 45, 21, 22, 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: 516 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: REAL300025241400 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C=CC1=NC=CO1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 26, 26, 26, 26, 26, 8, 14, 14, 20, 20, 34, 34, 34, 34, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 26, 20, 20, 34, 34] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 137 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241400 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241400 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241400/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241400 Building REAL300025241401 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241401' /scratch/stefan/7787021/working/building/REAL300025241401 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241401 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241401/0 /scratch/stefan/7787021/working/building/REAL300025241401 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/271 `/scratch/stefan/7787021/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1CCC1)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241401.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241401 none CC(CC1CCC1)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 5, 11, 22, 36, 36, 36, 4, 5, 3, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 48, 48, 48, 48, 48, 11, 11, 11, 11, 22, 22, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 48] 201 rigid atoms, others: [48, 17, 15, 11, 12, 13, 14, 45, 16, 49, 50, 51, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 52, 53, 54]) total number of confs: 218 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: REAL300025241401 none CC(CC1CCC1)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 92, 150, 178, 201, 201, 201, 87, 92, 79, 87, 48, 48, 48, 48, 48, 48, 31, 48, 13, 1, 1, 1, 1, 1, 1, 1, 150, 150, 150, 150, 178, 178, 201, 201, 201, 201, 201, 201, 201, 87, 87, 87, 79, 79, 48, 48, 48, 48, 48, 48, 48, 31, 31, 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: 952 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: REAL300025241401 none CC(CC1CCC1)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 10, 18, 18, 20, 20, 31, 36, 36, 36, 36, 36, 36, 36, 58, 99, 201, 201, 201, 201, 201, 10, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 31, 31, 36, 36, 36, 36, 36, 36, 36, 58, 58, 201] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 39, 34, 35, 36, 38, 37] set([0, 1, 7, 8, 9, 10, 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, 49, 50, 51, 52, 53, 54]) total number of confs: 525 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241401 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241401 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241401/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241401 Building REAL300025241402 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241402' /scratch/stefan/7787021/working/building/REAL300025241402 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241402 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241402/0 /scratch/stefan/7787021/working/building/REAL300025241402 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/272 `/scratch/stefan/7787021/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CC(C)(C)C1) `REAL300025241402.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241402 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 104, 64, 64, 64, 64, 64, 56, 31, 56, 13, 1, 1, 1, 1, 1, 1, 1, 129, 201, 201, 201, 201, 201, 201, 201, 129, 129, 129, 104, 104, 64, 64, 64, 64, 64, 64, 64, 31, 31, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 730 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: REAL300025241402 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 20, 24, 35, 35, 35, 35, 35, 36, 36, 71, 112, 201, 201, 201, 201, 201, 1, 10, 1, 1, 1, 1, 1, 1, 20, 20, 20, 24, 24, 35, 35, 35, 35, 35, 35, 35, 71, 71, 201, 1, 2, 2, 2, 2, 2, 2, 1, 1] 201 rigid atoms, others: [41, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 534 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: REAL300025241402 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 19, 64, 64, 64, 64, 64, 8, 19, 19, 35, 35, 35, 35, 35, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 64, 35, 35, 35, 35, 35, 35, 35, 35, 35] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241402 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241402 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241402/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241402 Building REAL300025241403 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241403' /scratch/stefan/7787021/working/building/REAL300025241403 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241403 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241403/0 /scratch/stefan/7787021/working/building/REAL300025241403 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/273 `/scratch/stefan/7787021/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CCC1=NNC=C1) `REAL300025241403.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241403 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CCC1=NNC=C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 82, 44, 44, 44, 44, 44, 44, 29, 44, 13, 1, 1, 1, 1, 1, 1, 1, 108, 145, 145, 145, 145, 201, 201, 201, 201, 108, 108, 108, 82, 82, 44, 44, 44, 44, 44, 44, 44, 29, 29, 1, 145, 145, 145, 145, 201, 201, 201] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 675 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: REAL300025241403 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CCC1=NNC=C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 20, 28, 38, 38, 38, 38, 38, 38, 38, 64, 107, 201, 201, 201, 201, 201, 6, 12, 6, 1, 1, 1, 1, 1, 1, 20, 20, 20, 28, 28, 38, 38, 38, 38, 38, 38, 38, 64, 64, 201, 6, 6, 6, 6, 1, 1, 1] 201 rigid atoms, others: [46, 47, 48, 21, 22, 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, 44, 45]) total number of confs: 546 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: REAL300025241403 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CCC1=NNC=C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 44, 44, 44, 44, 44, 7, 13, 13, 13, 13, 38, 38, 38, 38, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 44, 13, 13, 13, 13, 38, 38, 38] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241403 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241403 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241403/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241403 Building REAL300025241404 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241404' /scratch/stefan/7787021/working/building/REAL300025241404 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241404 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241404/0 /scratch/stefan/7787021/working/building/REAL300025241404 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/274 `/scratch/stefan/7787021/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(O)CC(C)(C)C1) `REAL300025241404.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241404 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(O)CC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [131, 127, 88, 88, 88, 88, 88, 69, 29, 69, 13, 1, 1, 1, 1, 1, 1, 1, 131, 178, 178, 201, 201, 201, 201, 201, 201, 131, 131, 131, 127, 127, 88, 88, 88, 88, 88, 88, 88, 29, 29, 1, 603, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 603 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 1352 number of broken/clashed sets: 364 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241404 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(O)CC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 5, 8, 14, 22, 22, 22, 22, 22, 28, 28, 60, 102, 201, 201, 201, 201, 201, 1, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 14, 14, 22, 22, 22, 22, 22, 22, 22, 60, 60, 201, 6, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 603 rigid atoms, others: [43, 44, 18, 51, 20, 21, 22, 23, 24, 25, 26, 52] 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, 42, 45, 46, 47, 48, 49, 50]) total number of confs: 508 number of broken/clashed sets: 364 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241404 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(O)CC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 29, 88, 88, 88, 88, 88, 7, 14, 14, 22, 22, 22, 22, 22, 22, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 16, 16, 88, 66, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 294 number of broken/clashed sets: 364 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241404 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241404 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241404/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241404 Building REAL300025241405 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241405' /scratch/stefan/7787021/working/building/REAL300025241405 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241405 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241405/0 /scratch/stefan/7787021/working/building/REAL300025241405 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/275 `/scratch/stefan/7787021/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CC1(C2CC2)CC1) `REAL300025241405.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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: REAL300025241405 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CC1(C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', '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', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 68, 41, 41, 41, 41, 41, 41, 28, 41, 12, 1, 1, 1, 1, 1, 1, 1, 104, 152, 152, 156, 182, 201, 201, 182, 182, 104, 104, 104, 68, 68, 41, 41, 41, 41, 41, 41, 41, 28, 28, 1, 156, 156, 201, 201, 201, 201, 201, 182, 182, 182, 182] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 767 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: REAL300025241405 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CC1(C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', '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', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 21, 32, 37, 37, 37, 37, 37, 37, 37, 63, 100, 201, 201, 201, 201, 201, 8, 14, 6, 1, 1, 1, 1, 6, 6, 21, 21, 21, 32, 32, 37, 37, 37, 37, 37, 37, 37, 63, 63, 201, 8, 8, 1, 1, 1, 1, 1, 6, 6, 6, 6] 201 rigid atoms, others: [44, 45, 46, 47, 48, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 49, 50, 51, 52]) total number of confs: 542 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: REAL300025241405 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CC1(C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', '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', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 14, 23, 27, 27, 27, 27, 27, 27, 27, 52, 85, 182, 182, 182, 182, 182, 5, 9, 1, 1, 1, 6, 6, 1, 1, 14, 14, 14, 23, 23, 27, 27, 27, 27, 27, 27, 27, 52, 52, 182, 5, 5, 6, 6, 6, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [49, 50, 51, 20, 21, 22, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 484 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: REAL300025241405 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CC1(C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', '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', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 41, 41, 41, 41, 41, 7, 15, 15, 19, 27, 37, 37, 27, 27, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 41, 19, 19, 37, 37, 37, 37, 37, 27, 27, 27, 27] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 184 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241405 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241405 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241405/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241405 Building REAL300025241406 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241406' /scratch/stefan/7787021/working/building/REAL300025241406 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241406 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241406/0 /scratch/stefan/7787021/working/building/REAL300025241406 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/276 `/scratch/stefan/7787021/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@@H]1CC1(F)F) `REAL300025241406.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241406 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@@H]1CC1(F)F NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 86, 51, 51, 51, 51, 51, 51, 36, 51, 12, 1, 1, 1, 1, 1, 1, 1, 136, 170, 170, 201, 201, 201, 201, 201, 136, 136, 136, 86, 86, 51, 51, 51, 51, 51, 51, 51, 36, 36, 1, 201, 201] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 791 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: REAL300025241406 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@@H]1CC1(F)F NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 16, 27, 34, 34, 34, 34, 34, 34, 34, 57, 100, 201, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 27, 27, 34, 34, 34, 34, 34, 34, 34, 57, 57, 201, 1, 1] 201 rigid atoms, others: [41, 42, 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: 503 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: REAL300025241406 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@@H]1CC1(F)F NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 51, 51, 51, 51, 51, 11, 22, 22, 34, 34, 34, 34, 34, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 34, 34] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42]) total number of confs: 184 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241406 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241406 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241406/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241406 Building REAL300025241407 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241407' /scratch/stefan/7787021/working/building/REAL300025241407 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241407 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241407/0 /scratch/stefan/7787021/working/building/REAL300025241407 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/277 `/scratch/stefan/7787021/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1C2C3CC1CC32) `REAL300025241407.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241407 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1C2C3CC1CC32 NO_LONG_NAME dock atom types: ['C.3', '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', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 118, 91, 91, 91, 91, 91, 67, 28, 67, 13, 1, 1, 1, 1, 1, 1, 1, 158, 191, 191, 201, 201, 201, 201, 201, 201, 158, 158, 158, 118, 118, 91, 91, 91, 91, 91, 91, 91, 28, 28, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 686 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: REAL300025241407 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1C2C3CC1CC32 NO_LONG_NAME dock atom types: ['C.3', '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', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 10, 16, 23, 23, 23, 23, 23, 30, 30, 64, 112, 201, 201, 201, 201, 201, 1, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 16, 16, 23, 23, 23, 23, 23, 23, 23, 64, 64, 201, 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: 516 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: REAL300025241407 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1C2C3CC1CC32 NO_LONG_NAME dock atom types: ['C.3', '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', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 35, 91, 91, 91, 91, 91, 11, 20, 20, 23, 23, 23, 23, 23, 23, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 18, 18, 91, 23, 23, 23, 23, 23, 23, 23, 23, 23] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 239 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241407 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241407 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241407/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241407 Building REAL300025241408 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241408' /scratch/stefan/7787021/working/building/REAL300025241408 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241408 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241408/0 /scratch/stefan/7787021/working/building/REAL300025241408 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/278 `/scratch/stefan/7787021/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@@H](O)C1CCCC1) `REAL300025241408.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241408 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@@H](O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [121, 76, 50, 50, 50, 50, 50, 50, 27, 50, 11, 1, 1, 1, 1, 1, 1, 1, 121, 167, 167, 180, 180, 180, 201, 201, 201, 201, 121, 121, 121, 76, 76, 50, 50, 50, 50, 50, 50, 50, 27, 27, 1, 540, 201, 201, 201, 201, 201, 201, 201, 201, 201] 603 rigid atoms, others: [42, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 1320 number of broken/clashed sets: 218 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241408 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@@H](O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 23, 30, 38, 38, 38, 38, 38, 38, 38, 68, 106, 201, 201, 201, 201, 201, 4, 14, 1, 4, 4, 1, 1, 1, 1, 1, 23, 23, 23, 30, 30, 38, 38, 38, 38, 38, 38, 38, 68, 68, 201, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1] 603 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 544 number of broken/clashed sets: 218 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241408 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@@H](O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 14, 50, 50, 50, 50, 50, 9, 19, 19, 26, 26, 26, 38, 38, 38, 38, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 78, 38, 38, 38, 38, 38, 38, 38, 38, 38] 603 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 39, 34, 35, 36, 38, 37] 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 296 number of broken/clashed sets: 218 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241408 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241408 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241408/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241408 Building REAL300025241409 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241409' /scratch/stefan/7787021/working/building/REAL300025241409 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241409 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241409/0 /scratch/stefan/7787021/working/building/REAL300025241409 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/279 `/scratch/stefan/7787021/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241409.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241409 none CC(=O)NCCC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 4, 7, 7, 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 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, 172, 134, 94, 84, 94, 56, 84, 35, 35, 35, 35, 35, 35, 26, 35, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 172, 172, 134, 134, 84, 84, 84, 56, 56, 35, 35, 35, 35, 35, 35, 35, 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: 869 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: REAL300025241409 none CC(=O)NCCC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 4, 7, 7, 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 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, 20, 7, 6, 7, 2, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 26, 26, 20, 20, 6, 6, 6, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 35] 201 rigid atoms, others: [45, 43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241409 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241409 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241409/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241409 Building REAL300025241410 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241410' /scratch/stefan/7787021/working/building/REAL300025241410 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241410 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241410/0 /scratch/stefan/7787021/working/building/REAL300025241410 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/280 `/scratch/stefan/7787021/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CNC(=O)N1) `REAL300025241410.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241410 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CNC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 75, 48, 48, 48, 48, 48, 47, 28, 47, 13, 1, 1, 1, 1, 1, 1, 1, 94, 145, 145, 201, 201, 201, 201, 201, 94, 94, 94, 75, 75, 48, 48, 48, 48, 48, 48, 48, 28, 28, 1, 201, 201, 201] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 654 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: REAL300025241410 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CNC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 11, 19, 27, 32, 32, 32, 32, 32, 34, 34, 61, 100, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 1, 19, 19, 19, 27, 27, 32, 32, 32, 32, 32, 32, 32, 61, 61, 201, 1, 1, 1] 201 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: 512 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: REAL300025241410 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CNC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 12, 48, 48, 48, 48, 48, 9, 17, 17, 32, 32, 32, 32, 32, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 48, 32, 32, 32] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241410 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241410 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241410/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241410 Building REAL300025241411 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241411' /scratch/stefan/7787021/working/building/REAL300025241411 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241411 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241411/0 /scratch/stefan/7787021/working/building/REAL300025241411 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/281 `/scratch/stefan/7787021/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCC1C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241411.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241411 none CC1CCCC1C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 13, 10, 13, 5, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 45, 143, 143, 143, 143, 143, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 24, 24, 143] 201 rigid atoms, others: [16, 45, 43, 44, 10, 11, 12, 13, 14, 15, 48, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 49, 50, 51]) total number of confs: 296 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: REAL300025241411 none CC1CCCC1C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 194, 201, 184, 194, 143, 143, 143, 143, 143, 106, 36, 106, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 194, 194, 194, 184, 184, 143, 143, 143, 143, 143, 143, 143, 36, 36, 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: 659 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: REAL300025241411 none CC1CCCC1C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 201 conformations 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, 5, 5, 9, 15, 15, 15, 15, 15, 27, 27, 74, 118, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 15, 15, 15, 15, 15, 15, 15, 74, 74, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 35, 36, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 495 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241411 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241411 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241411/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241411 Building REAL300025241412 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241412' /scratch/stefan/7787021/working/building/REAL300025241412 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241412 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241412/0 /scratch/stefan/7787021/working/building/REAL300025241412 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/282 `/scratch/stefan/7787021/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C)(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025241412.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241412 none CC1CCC(C)(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 12, 10, 10, 4, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 52, 134, 134, 134, 134, 134, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 26, 26, 134, 12, 12] 201 rigid atoms, others: [16, 45, 11, 44, 10, 43, 12, 13, 14, 15, 48, 49, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 50, 51, 52, 53, 54]) total number of confs: 280 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: REAL300025241412 none CC1CCC(C)(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 191, 201, 191, 191, 175, 191, 134, 134, 134, 134, 134, 94, 32, 94, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 191, 191, 191, 175, 175, 134, 134, 134, 134, 134, 134, 134, 32, 32, 1, 201, 201] 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]) total number of confs: 653 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: REAL300025241412 none CC1CCC(C)(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 3, 8, 12, 12, 12, 12, 12, 22, 22, 74, 114, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 8, 8, 12, 12, 12, 12, 12, 12, 12, 74, 74, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 53, 54, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 507 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241412 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241412 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241412/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241412 Building REAL300025241413 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241413' /scratch/stefan/7787021/working/building/REAL300025241413 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241413 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241413/0 /scratch/stefan/7787021/working/building/REAL300025241413 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/283 `/scratch/stefan/7787021/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241413.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241413 none C=C(C)CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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: [1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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: [201, 201, 201, 107, 103, 107, 95, 103, 59, 59, 59, 59, 59, 59, 30, 59, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 103, 103, 103, 95, 95, 59, 59, 59, 59, 59, 59, 59, 30, 30, 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: 881 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: REAL300025241413 none C=C(C)CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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: [1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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: [38, 31, 38, 9, 7, 9, 3, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 13, 59, 59, 59, 59, 59, 38, 38, 38, 38, 38, 31, 31, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 59] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241413 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241413 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241413/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241413 Building REAL300025241414 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241414' /scratch/stefan/7787021/working/building/REAL300025241414 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241414 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241414/0 /scratch/stefan/7787021/working/building/REAL300025241414 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/284 `/scratch/stefan/7787021/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CCC(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC1) `REAL300025241414.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241414 none CC1=CCC(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 14, 8, 14, 4, 8, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 23, 72, 72, 72, 72, 72, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 72, 26, 26, 26, 26] 201 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 214 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: REAL300025241414 none CC1=CCC(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 139, 111, 139, 96, 111, 72, 72, 72, 72, 72, 58, 29, 58, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 111, 111, 111, 96, 96, 72, 72, 72, 72, 72, 72, 72, 29, 29, 1, 201, 201, 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]) total number of confs: 747 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: REAL300025241414 none CC1=CCC(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 12, 12, 19, 26, 26, 26, 26, 26, 33, 33, 61, 99, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 1, 12, 12, 12, 19, 19, 26, 26, 26, 26, 26, 26, 26, 61, 61, 201, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 33, 49, 50, 51, 52, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 500 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241414 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241414 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241414/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241414 Building REAL300025241415 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241415' /scratch/stefan/7787021/working/building/REAL300025241415 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241415 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241415/0 /scratch/stefan/7787021/working/building/REAL300025241415 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/285 `/scratch/stefan/7787021/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSCC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241415.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241415 none CCSCC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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: [201, 201, 173, 117, 115, 117, 100, 115, 58, 58, 58, 58, 58, 58, 31, 58, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 173, 173, 115, 115, 115, 100, 100, 58, 58, 58, 58, 58, 58, 58, 31, 31, 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: 842 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: REAL300025241415 none CCSCC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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: [49, 37, 16, 6, 5, 6, 4, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 11, 58, 58, 58, 58, 58, 49, 49, 49, 49, 49, 16, 16, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 58] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241415 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241415 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241415/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241415 Building REAL300025241416 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241416' /scratch/stefan/7787021/working/building/REAL300025241416 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241416 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241416/0 /scratch/stefan/7787021/working/building/REAL300025241416 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/286 `/scratch/stefan/7787021/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(C)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241416.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241416 none CC(C)=C(C)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.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', 'H'] dock atom type numbers: [5, 1, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 201, 135, 143, 112, 135, 74, 74, 74, 74, 74, 60, 27, 60, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 135, 135, 135, 112, 112, 74, 74, 74, 74, 74, 74, 74, 27, 27, 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: 774 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: REAL300025241416 none CC(C)=C(C)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.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', 'H'] dock atom type numbers: [5, 1, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 22, 7, 17, 4, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 27, 74, 74, 74, 74, 74, 22, 22, 22, 22, 22, 22, 22, 22, 22, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 74] 201 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241416 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241416 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241416/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241416 Building REAL300025241417 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241417' /scratch/stefan/7787021/working/building/REAL300025241417 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241417 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241417/0 /scratch/stefan/7787021/working/building/REAL300025241417 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/287 `/scratch/stefan/7787021/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C(F)(F)C(F)F) `REAL300025241417.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241417 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C(F)(F)C(F)F NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 15, 15, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 102, 64, 64, 64, 64, 64, 60, 35, 60, 13, 1, 1, 1, 1, 1, 1, 1, 131, 201, 201, 201, 201, 201, 201, 201, 131, 131, 131, 102, 102, 64, 64, 64, 64, 64, 64, 64, 35, 35, 1, 201] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 739 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: REAL300025241417 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C(F)(F)C(F)F NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 15, 15, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 13, 64, 64, 64, 64, 64, 8, 22, 22, 22, 22, 22, 34, 34, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 64, 34] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241417 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241417 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241417/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241417 Building REAL300025241418 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241418' /scratch/stefan/7787021/working/building/REAL300025241418 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241418 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241418/0 /scratch/stefan/7787021/working/building/REAL300025241418 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/288 `/scratch/stefan/7787021/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(O)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241418.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241418 none CCCC(O)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 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, 159, 128, 159, 104, 128, 92, 104, 60, 60, 60, 60, 60, 57, 29, 57, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 159, 477, 104, 104, 104, 92, 92, 60, 60, 60, 60, 60, 60, 60, 29, 29, 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: 1411 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: REAL300025241418 none CCCC(O)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 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, 33, 16, 9, 16, 6, 9, 4, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 60, 60, 60, 60, 60, 37, 37, 37, 37, 37, 34, 34, 16, 48, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 60] 603 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48]) total number of confs: 318 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241418 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241418 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241418/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241418 Building REAL300025241419 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241419' /scratch/stefan/7787021/working/building/REAL300025241419 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241419 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241419/0 /scratch/stefan/7787021/working/building/REAL300025241419 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/289 `/scratch/stefan/7787021/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(O)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241419.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241419 none CCCCC(O)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 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, 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, 167, 126, 167, 107, 126, 87, 107, 55, 55, 55, 55, 55, 54, 29, 54, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 198, 198, 167, 501, 107, 107, 107, 87, 87, 55, 55, 55, 55, 55, 55, 55, 29, 29, 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: 1452 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: REAL300025241419 none CCCCC(O)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 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, 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, 35, 17, 9, 17, 6, 9, 4, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 55, 55, 55, 55, 55, 38, 38, 38, 38, 38, 37, 37, 36, 36, 17, 51, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 55] 603 rigid atoms, others: [16, 45, 43, 44, 10, 11, 12, 13, 14, 15, 48, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 49, 50, 51]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241419 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241419 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241419/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241419 Building REAL300025241420 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241420' /scratch/stefan/7787021/working/building/REAL300025241420 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241420 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241420/0 /scratch/stefan/7787021/working/building/REAL300025241420 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/290 `/scratch/stefan/7787021/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(C)O) `REAL300025241420.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241420 none COC(C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(C)O 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', 'C.3', 'C.3', 'N.am', '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, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 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] 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, 136, 116, 136, 101, 116, 68, 68, 68, 68, 68, 60, 30, 60, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 116, 116, 116, 101, 101, 68, 68, 68, 68, 68, 68, 68, 30, 30, 1, 201, 201, 201, 201, 603] 603 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]) total number of confs: 1442 number of broken/clashed sets: 122 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241420 none COC(C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(C)O 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', 'C.3', 'C.3', 'N.am', '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, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 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] 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, 23, 12, 7, 12, 4, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 20, 68, 68, 68, 68, 68, 23, 29, 29, 27, 27, 27, 23, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 68, 29, 29, 29, 29, 87] 603 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 40, 41, 39] 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 330 number of broken/clashed sets: 122 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241420 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241420 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241420/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241420 Building REAL300025241421 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241421' /scratch/stefan/7787021/working/building/REAL300025241421 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241421 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241421/0 /scratch/stefan/7787021/working/building/REAL300025241421 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/291 `/scratch/stefan/7787021/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CSC1CC1) `REAL300025241421.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241421 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CSC1CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 48, 34, 34, 34, 34, 34, 34, 25, 34, 13, 1, 1, 1, 1, 1, 1, 1, 72, 109, 109, 174, 198, 201, 201, 72, 72, 72, 48, 48, 34, 34, 34, 34, 34, 34, 34, 25, 25, 1, 174, 174, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 762 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: REAL300025241421 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CSC1CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 22, 35, 38, 39, 39, 39, 39, 39, 39, 39, 60, 105, 201, 201, 201, 201, 201, 13, 22, 6, 1, 1, 1, 1, 35, 35, 35, 38, 38, 39, 39, 39, 39, 39, 39, 39, 60, 60, 201, 13, 13, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 513 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: REAL300025241421 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CSC1CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 34, 34, 34, 34, 34, 7, 11, 11, 23, 31, 39, 39, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 34, 23, 23, 39, 39, 39, 39, 39] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 182 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241421 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241421 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241421/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241421 Building REAL300025241422 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241422' /scratch/stefan/7787021/working/building/REAL300025241422 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241422 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241422/0 /scratch/stefan/7787021/working/building/REAL300025241422 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/292 `/scratch/stefan/7787021/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CCCC1CCC1) `REAL300025241422.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241422 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CCCC1CCC1 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 78, 41, 41, 41, 41, 41, 38, 32, 38, 12, 1, 1, 1, 1, 1, 1, 1, 96, 107, 107, 107, 110, 113, 201, 201, 201, 96, 96, 96, 78, 78, 41, 41, 41, 41, 41, 41, 41, 32, 32, 1, 107, 107, 110, 110, 113, 113, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 815 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: REAL300025241422 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CCCC1CCC1 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 19, 19, 19, 19, 19, 34, 34, 68, 104, 201, 201, 201, 201, 201, 9, 11, 7, 5, 1, 1, 1, 1, 1, 11, 11, 11, 17, 17, 19, 19, 19, 19, 19, 19, 19, 68, 68, 201, 9, 9, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [54, 48, 49, 50, 51, 52, 53, 22, 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, 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: 509 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: REAL300025241422 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CCCC1CCC1 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 18, 41, 41, 41, 41, 41, 7, 8, 8, 8, 9, 11, 19, 19, 19, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 41, 8, 8, 9, 9, 11, 11, 19, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241422 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241422 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241422/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241422 Building REAL300025241423 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241423' /scratch/stefan/7787021/working/building/REAL300025241423 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241423 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241423/0 /scratch/stefan/7787021/working/building/REAL300025241423 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/293 `/scratch/stefan/7787021/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(O)CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241423.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241423 none CCC(O)CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 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] 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, 164, 201, 140, 114, 140, 80, 114, 48, 48, 48, 48, 48, 47, 29, 47, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 603, 164, 164, 114, 114, 114, 80, 80, 48, 48, 48, 48, 48, 48, 48, 29, 29, 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: 1500 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: REAL300025241423 none CCC(O)CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 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] 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: [39, 35, 23, 35, 12, 7, 12, 3, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 13, 48, 48, 48, 48, 48, 39, 39, 39, 39, 39, 35, 105, 23, 23, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 48] 603 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48]) total number of confs: 355 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241423 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241423 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241423/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241423 Building REAL300025241424 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241424' /scratch/stefan/7787021/working/building/REAL300025241424 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241424 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241424/0 /scratch/stefan/7787021/working/building/REAL300025241424 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/294 `/scratch/stefan/7787021/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(Cl)=CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241424.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241424 none CC(Cl)=CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'Cl', 'C.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'] dock atom type numbers: [5, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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: [201, 201, 201, 161, 148, 161, 112, 148, 79, 79, 79, 79, 79, 69, 30, 69, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 148, 148, 148, 112, 112, 79, 79, 79, 79, 79, 79, 79, 30, 30, 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: 783 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: REAL300025241424 none CC(Cl)=CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'Cl', 'C.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'] dock atom type numbers: [5, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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: [26, 26, 26, 12, 7, 12, 4, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 20, 79, 79, 79, 79, 79, 26, 26, 26, 26, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 79] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42]) total number of confs: 206 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241424 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241424 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241424/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241424 Building REAL300025241425 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241425' /scratch/stefan/7787021/working/building/REAL300025241425 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241425 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241425/0 /scratch/stefan/7787021/working/building/REAL300025241425 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/295 `/scratch/stefan/7787021/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241425.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241425 none CC=CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [201, 201, 201, 180, 201, 124, 180, 77, 77, 77, 77, 77, 67, 32, 67, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 180, 180, 180, 124, 124, 77, 77, 77, 77, 77, 77, 77, 32, 32, 1] 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]) total number of confs: 792 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: REAL300025241425 none CC=CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [34, 34, 17, 10, 17, 4, 10, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 19, 77, 77, 77, 77, 77, 34, 34, 34, 34, 34, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 77] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 39] 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, 40, 41, 42]) total number of confs: 227 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241425 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241425 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241425/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241425 Building REAL300025241426 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241426' /scratch/stefan/7787021/working/building/REAL300025241426 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241426 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241426/0 /scratch/stefan/7787021/working/building/REAL300025241426 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/296 `/scratch/stefan/7787021/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CNC(=O)N1C) `REAL300025241426.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241426 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CNC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 134, 86, 86, 86, 86, 86, 67, 30, 67, 13, 1, 1, 1, 1, 1, 1, 1, 172, 194, 194, 201, 201, 201, 201, 201, 201, 172, 172, 172, 134, 134, 86, 86, 86, 86, 86, 86, 86, 30, 30, 1, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 754 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: REAL300025241426 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CNC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 13, 19, 27, 27, 27, 27, 27, 35, 35, 71, 115, 201, 201, 201, 201, 201, 1, 5, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 19, 19, 27, 27, 27, 27, 27, 27, 27, 71, 71, 201, 1, 1, 1, 1, 2, 2, 2] 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, 46, 47, 48]) total number of confs: 533 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: REAL300025241426 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CNC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 25, 86, 86, 86, 86, 86, 12, 20, 20, 27, 27, 27, 27, 27, 27, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 86, 27, 27, 27, 27, 27, 27, 27] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 221 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241426 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241426 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241426/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241426 Building REAL300025241427 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241427' /scratch/stefan/7787021/working/building/REAL300025241427 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241427 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241427/0 /scratch/stefan/7787021/working/building/REAL300025241427 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/297 `/scratch/stefan/7787021/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)(F)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241427.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241427 none CCC(F)(F)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [201, 201, 186, 201, 201, 169, 186, 128, 169, 82, 82, 82, 82, 82, 63, 28, 63, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 169, 169, 169, 128, 128, 82, 82, 82, 82, 82, 82, 82, 28, 28, 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: 763 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: REAL300025241427 none CCC(F)(F)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [27, 26, 18, 26, 26, 9, 18, 4, 9, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 28, 82, 82, 82, 82, 82, 27, 27, 27, 27, 27, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 82] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241427 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241427 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241427/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241427 Building REAL300025241428 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241428' /scratch/stefan/7787021/working/building/REAL300025241428 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241428 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241428/0 /scratch/stefan/7787021/working/building/REAL300025241428 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/298 `/scratch/stefan/7787021/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CCCCC1F) `REAL300025241428.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241428 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CCCCC1F NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 99, 69, 69, 69, 69, 69, 56, 29, 56, 13, 1, 1, 1, 1, 1, 1, 1, 131, 180, 180, 201, 201, 201, 201, 201, 201, 131, 131, 131, 99, 99, 69, 69, 69, 69, 69, 69, 69, 29, 29, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 737 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: REAL300025241428 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CCCCC1F NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 13, 18, 22, 22, 22, 22, 22, 26, 26, 55, 102, 201, 201, 201, 201, 201, 1, 5, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 18, 18, 22, 22, 22, 22, 22, 22, 22, 55, 55, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 503 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: REAL300025241428 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CCCCC1F NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 10, 22, 69, 69, 69, 69, 69, 9, 17, 17, 22, 22, 22, 22, 22, 22, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 69, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 186 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241428 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241428 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241428/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241428 Building REAL300025241429 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241429' /scratch/stefan/7787021/working/building/REAL300025241429 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241429 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241429/0 /scratch/stefan/7787021/working/building/REAL300025241429 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/299 `/scratch/stefan/7787021/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(C)CC1F) `REAL300025241429.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241429 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(C)CC1F NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 128, 90, 90, 90, 90, 90, 77, 46, 77, 13, 1, 1, 1, 1, 1, 1, 1, 136, 201, 201, 201, 201, 201, 201, 136, 136, 136, 128, 128, 90, 90, 90, 90, 90, 90, 90, 46, 46, 1, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 738 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: REAL300025241429 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(C)CC1F NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 21, 21, 62, 103, 201, 201, 201, 201, 201, 1, 3, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 17, 17, 17, 17, 17, 17, 17, 62, 62, 201, 2, 2, 2, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 461 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: REAL300025241429 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(C)CC1F NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 30, 90, 90, 90, 90, 90, 10, 16, 16, 17, 17, 17, 17, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 90, 17, 17, 17, 17, 17, 17] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 205 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241429 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241429 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241429/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241429 Building REAL300025241430 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241430' /scratch/stefan/7787021/working/building/REAL300025241430 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241430 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241430/0 /scratch/stefan/7787021/working/building/REAL300025241430 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/300 `/scratch/stefan/7787021/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@H]1C[C@@H](O)C1) `REAL300025241430.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241430 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@H]1C[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 85, 50, 50, 50, 50, 50, 48, 30, 48, 13, 1, 1, 1, 1, 1, 1, 1, 128, 171, 171, 201, 201, 201, 201, 201, 201, 128, 128, 128, 85, 85, 50, 50, 50, 50, 50, 50, 50, 30, 30, 1, 201, 201, 603, 201, 201] 603 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 1363 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: REAL300025241430 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@H]1C[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 18, 24, 32, 32, 32, 32, 32, 33, 33, 59, 98, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 24, 24, 32, 32, 32, 32, 32, 32, 32, 59, 59, 201, 1, 1, 3, 1, 1] 603 rigid atoms, others: [42, 43, 45, 46, 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, 44]) total number of confs: 494 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: REAL300025241430 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@H]1C[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 14, 50, 50, 50, 50, 50, 8, 19, 19, 32, 32, 32, 32, 32, 32, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 32, 32, 96, 32, 32] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 279 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241430 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241430 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241430/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241430 Building REAL300025241431 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241431' /scratch/stefan/7787021/working/building/REAL300025241431 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241431 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241431/0 /scratch/stefan/7787021/working/building/REAL300025241431 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/301 `/scratch/stefan/7787021/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CC1CC1(C)C) `REAL300025241431.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241431 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CC1CC1(C)C NO_LONG_NAME dock atom types: ['C.3', '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', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 68, 44, 44, 44, 44, 44, 44, 28, 44, 13, 1, 1, 1, 1, 1, 1, 1, 109, 149, 149, 158, 201, 201, 201, 201, 109, 109, 109, 68, 68, 44, 44, 44, 44, 44, 44, 44, 28, 28, 1, 158, 158, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 771 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: REAL300025241431 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CC1CC1(C)C NO_LONG_NAME dock atom types: ['C.3', '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', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 20, 29, 37, 37, 37, 37, 37, 37, 37, 66, 101, 201, 201, 201, 201, 201, 5, 12, 1, 1, 1, 1, 1, 1, 20, 20, 20, 29, 29, 37, 37, 37, 37, 37, 37, 37, 66, 66, 201, 5, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2] 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, 46, 47, 48, 49, 50, 51]) total number of confs: 557 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: REAL300025241431 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CC1CC1(C)C NO_LONG_NAME dock atom types: ['C.3', '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', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 2, 2, 6, 11, 44, 44, 44, 44, 44, 9, 16, 16, 20, 37, 37, 37, 37, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 44, 20, 20, 37, 37, 37, 37, 37, 37, 37, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 189 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241431 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241431 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241431/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241431 Building REAL300025241432 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241432' /scratch/stefan/7787021/working/building/REAL300025241432 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241432 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241432/0 /scratch/stefan/7787021/working/building/REAL300025241432 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/302 `/scratch/stefan/7787021/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCCC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241432.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241432 none CCCCCCCC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 121, 120, 121, 97, 120, 58, 58, 58, 58, 58, 52, 42, 52, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 120, 120, 120, 97, 97, 58, 58, 58, 58, 58, 58, 58, 42, 42, 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: 829 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: REAL300025241432 none CCCCCCCC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 30, 10, 9, 10, 4, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 18, 58, 58, 58, 58, 58, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 30, 30, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 58] 201 rigid atoms, others: [48, 17, 11, 12, 13, 14, 47, 16, 49, 50, 51, 52, 53, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 54, 55, 56]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241432 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241432 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241432/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241432 Building REAL300025241433 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241433' /scratch/stefan/7787021/working/building/REAL300025241433 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241433 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241433/0 /scratch/stefan/7787021/working/building/REAL300025241433 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/303 `/scratch/stefan/7787021/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NC(N)=O)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241433.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241433 none CC(NC(N)=O)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 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, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 7, 4, 6, 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: [201, 165, 201, 201, 201, 201, 139, 165, 124, 139, 77, 77, 77, 77, 77, 64, 32, 64, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 139, 139, 139, 124, 124, 77, 77, 77, 77, 77, 77, 77, 32, 32, 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: 847 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: REAL300025241433 none CC(NC(N)=O)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 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, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 7, 4, 6, 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: [25, 14, 25, 31, 31, 31, 10, 14, 5, 10, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 23, 77, 77, 77, 77, 77, 25, 25, 25, 25, 31, 31, 31, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 13, 13, 77] 201 rigid atoms, others: [43, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47]) total number of confs: 254 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241433 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241433 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241433/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241433 Building REAL300025241434 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241434' /scratch/stefan/7787021/working/building/REAL300025241434 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241434 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241434/0 /scratch/stefan/7787021/working/building/REAL300025241434 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/304 `/scratch/stefan/7787021/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(O)CCOCC1) `REAL300025241434.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241434 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(O)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [158, 144, 92, 92, 92, 92, 92, 71, 30, 71, 13, 1, 1, 1, 1, 1, 1, 1, 158, 201, 201, 201, 201, 201, 201, 201, 201, 158, 158, 158, 144, 144, 92, 92, 92, 92, 92, 92, 92, 30, 30, 1, 603, 201, 201, 201, 201, 201, 201, 201, 201] 603 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 1358 number of broken/clashed sets: 529 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241434 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(O)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 3, 5, 10, 16, 16, 16, 16, 16, 28, 28, 72, 113, 201, 201, 201, 201, 201, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 16, 16, 16, 16, 16, 16, 16, 72, 72, 201, 6, 1, 1, 1, 1, 1, 1, 1, 1] 603 rigid atoms, others: [50, 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, 42]) total number of confs: 518 number of broken/clashed sets: 529 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241434 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(O)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 34, 92, 92, 92, 92, 92, 9, 16, 16, 16, 16, 16, 16, 16, 16, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 19, 19, 92, 48, 16, 16, 16, 16, 16, 16, 16, 16] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 269 number of broken/clashed sets: 529 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241434 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241434 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241434/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241434 Building REAL300025241435 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241435' /scratch/stefan/7787021/working/building/REAL300025241435 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241435 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241435/0 /scratch/stefan/7787021/working/building/REAL300025241435 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/305 `/scratch/stefan/7787021/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C#CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241435.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241435 none CN(C)C(=O)C#CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.1', 'C.1', '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, 8, 5, 1, 11, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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: [201, 201, 201, 201, 201, 201, 201, 167, 201, 139, 167, 87, 87, 87, 87, 87, 74, 30, 74, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 167, 167, 167, 139, 139, 87, 87, 87, 87, 87, 87, 87, 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: 745 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: REAL300025241435 none CN(C)C(=O)C#CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.1', 'C.1', '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, 8, 5, 1, 11, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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: [23, 20, 23, 20, 20, 20, 20, 9, 20, 4, 9, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 29, 87, 87, 87, 87, 87, 23, 23, 23, 23, 23, 23, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 16, 16, 87] 201 rigid atoms, others: [43, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47]) total number of confs: 228 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241435 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241435 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241435/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241435 Building REAL300025241436 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241436' /scratch/stefan/7787021/working/building/REAL300025241436 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241436 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241436/0 /scratch/stefan/7787021/working/building/REAL300025241436 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/306 `/scratch/stefan/7787021/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CCCC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241436.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241436 none C=C(C)CCCC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 140, 130, 56, 56, 56, 49, 56, 31, 31, 31, 31, 31, 31, 23, 31, 11, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 197, 197, 157, 157, 130, 130, 56, 56, 56, 49, 49, 31, 31, 31, 31, 31, 31, 31, 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: 996 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: REAL300025241436 none C=C(C)CCCC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 36, 52, 20, 14, 4, 4, 4, 3, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 31, 31, 31, 31, 31, 52, 52, 52, 52, 52, 35, 35, 24, 24, 14, 14, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 31] 201 rigid atoms, others: [16, 45, 43, 44, 10, 11, 12, 13, 14, 15, 48, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 49, 50, 51]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241436 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241436 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241436/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241436 Building REAL300025241437 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241437' /scratch/stefan/7787021/working/building/REAL300025241437 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241437 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241437/0 /scratch/stefan/7787021/working/building/REAL300025241437 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/307 `/scratch/stefan/7787021/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)=NN1C) `REAL300025241437.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241437 none CC1=NC(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)=NN1C 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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: [40, 40, 40, 11, 5, 11, 4, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 12, 49, 49, 49, 49, 49, 40, 40, 40, 40, 40, 40, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 49, 40, 40, 40] 201 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47]) total number of confs: 143 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: REAL300025241437 none CC1=NC(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)=NN1C 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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: [201, 201, 201, 121, 88, 121, 86, 88, 49, 49, 49, 49, 49, 49, 29, 49, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 88, 88, 88, 86, 86, 49, 49, 49, 49, 49, 49, 49, 29, 29, 1, 201, 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]) total number of confs: 624 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: REAL300025241437 none CC1=NC(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)=NN1C 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 1, 12, 12, 19, 19, 32, 40, 40, 40, 40, 40, 41, 41, 64, 116, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 19, 19, 19, 32, 32, 40, 40, 40, 40, 40, 40, 40, 64, 64, 201, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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, 45, 46, 47]) total number of confs: 549 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241437 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241437 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241437/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241437 Building REAL300025241438 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241438' /scratch/stefan/7787021/working/building/REAL300025241438 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241438 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241438/0 /scratch/stefan/7787021/working/building/REAL300025241438 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/308 `/scratch/stefan/7787021/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(C)CC(F)C1) `REAL300025241438.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241438 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(C)CC(F)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.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, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 96, 96, 96, 96, 96, 69, 30, 69, 13, 1, 1, 1, 1, 1, 1, 1, 135, 201, 201, 201, 201, 201, 201, 201, 135, 135, 135, 135, 135, 96, 96, 96, 96, 96, 96, 96, 30, 30, 1, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 701 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: REAL300025241438 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(C)CC(F)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.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, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 8, 13, 13, 13, 13, 13, 25, 25, 64, 110, 201, 201, 201, 201, 201, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 13, 13, 13, 13, 13, 13, 13, 64, 64, 201, 2, 2, 2, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 495 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: REAL300025241438 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(C)CC(F)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.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, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 39, 96, 96, 96, 96, 96, 6, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 20, 20, 96, 13, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 224 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241438 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241438 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241438/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241438 Building REAL300025241439 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241439' /scratch/stefan/7787021/working/building/REAL300025241439 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241439 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241439/0 /scratch/stefan/7787021/working/building/REAL300025241439 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/309 `/scratch/stefan/7787021/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)N1) `REAL300025241439.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241439 none CCC1=CC=C(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)N1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 9, 5, 9, 4, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 37, 37, 37, 37, 37, 20, 36, 36, 36, 36, 36, 20, 20, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 37, 20] 201 rigid atoms, others: [45, 43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 49]) total number of confs: 194 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: REAL300025241439 none CCC1=CC=C(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)N1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 77, 63, 77, 59, 63, 37, 37, 37, 37, 37, 37, 26, 37, 13, 1, 1, 1, 1, 1, 1, 1, 147, 201, 201, 201, 201, 201, 147, 147, 63, 63, 63, 59, 59, 37, 37, 37, 37, 37, 37, 37, 26, 26, 1, 147] 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, 49]) total number of confs: 757 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: REAL300025241439 none CCC1=CC=C(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)N1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 16, 20, 20, 20, 20, 20, 20, 20, 32, 55, 147, 147, 147, 147, 147, 1, 3, 3, 3, 3, 3, 1, 1, 11, 11, 11, 16, 16, 20, 20, 20, 20, 20, 20, 20, 32, 32, 147, 1] 201 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: 325 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241439 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241439 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241439/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241439 Building REAL300025241440 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241440' /scratch/stefan/7787021/working/building/REAL300025241440 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241440 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241440/0 /scratch/stefan/7787021/working/building/REAL300025241440 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/310 `/scratch/stefan/7787021/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C#CC1CCCO1) `REAL300025241440.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241440 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C#CC1CCCO1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.1', 'C.1', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 123, 83, 83, 83, 83, 83, 59, 30, 59, 13, 1, 1, 1, 1, 1, 1, 1, 147, 201, 201, 201, 201, 201, 201, 201, 201, 147, 147, 147, 123, 123, 83, 83, 83, 83, 83, 83, 83, 30, 30, 1, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 697 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: REAL300025241440 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C#CC1CCCO1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.1', 'C.1', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 12, 18, 18, 18, 18, 18, 25, 25, 55, 102, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 12, 18, 18, 18, 18, 18, 18, 18, 55, 55, 201, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 42, 43, 44, 45, 46, 47, 48, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 486 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: REAL300025241440 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C#CC1CCCO1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.1', 'C.1', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 5, 5, 15, 32, 83, 83, 83, 83, 83, 9, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 83, 18, 18, 18, 18, 18, 18, 18] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241440 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241440 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241440/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241440 Building REAL300025241441 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241441' /scratch/stefan/7787021/working/building/REAL300025241441 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241441 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241441/0 /scratch/stefan/7787021/working/building/REAL300025241441 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/311 `/scratch/stefan/7787021/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241441.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241441 none C[C@@H]1C[C@H]1C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 7, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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: [31, 31, 31, 31, 16, 31, 9, 16, 4, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 19, 64, 64, 64, 64, 64, 31, 31, 31, 31, 31, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 64] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45]) total number of confs: 200 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: REAL300025241441 none C[C@@H]1C[C@H]1C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 7, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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: [201, 201, 201, 201, 158, 201, 131, 158, 99, 131, 64, 64, 64, 64, 64, 56, 30, 56, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 131, 131, 131, 99, 99, 64, 64, 64, 64, 64, 64, 64, 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: 779 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: REAL300025241441 none C[C@@H]1C[C@H]1C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 7, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 8, 8, 14, 14, 21, 31, 31, 31, 31, 31, 33, 33, 68, 105, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 14, 14, 14, 21, 21, 31, 31, 31, 31, 31, 31, 31, 68, 68, 201] 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: 510 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241441 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241441 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241441/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241441 Building REAL300025241442 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241442' /scratch/stefan/7787021/working/building/REAL300025241442 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241442 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241442/0 /scratch/stefan/7787021/working/building/REAL300025241442 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/312 `/scratch/stefan/7787021/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(C)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241442.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241442 none CNC(=O)NC(C)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 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, 4, 7, 6, 4, 7, 7, 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: [201, 201, 201, 201, 191, 141, 191, 123, 141, 105, 123, 65, 65, 65, 65, 65, 58, 30, 58, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 191, 191, 191, 191, 123, 123, 123, 105, 105, 65, 65, 65, 65, 65, 65, 65, 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: 887 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: REAL300025241442 none CNC(=O)NC(C)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 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, 4, 7, 6, 4, 7, 7, 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: [38, 28, 28, 28, 19, 12, 19, 8, 12, 4, 8, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 22, 65, 65, 65, 65, 65, 38, 38, 38, 38, 28, 19, 19, 19, 19, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 65] 201 rigid atoms, others: [45, 43, 41, 42, 11, 12, 13, 14, 15, 16, 17, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50]) total number of confs: 255 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241442 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241442 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241442/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241442 Building REAL300025241443 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241443' /scratch/stefan/7787021/working/building/REAL300025241443 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241443 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241443/0 /scratch/stefan/7787021/working/building/REAL300025241443 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/313 `/scratch/stefan/7787021/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=NN=C1C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241443.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241443 none CCN1C=NN=C1C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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, 8, 1, 8, 8, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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: [43, 26, 26, 26, 26, 26, 10, 8, 10, 4, 8, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 18, 66, 66, 66, 66, 66, 43, 43, 43, 43, 43, 26, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 66] 201 rigid atoms, others: [43, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47]) total number of confs: 264 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: REAL300025241443 none CCN1C=NN=C1C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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, 8, 1, 8, 8, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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: [201, 198, 198, 198, 198, 198, 155, 147, 155, 120, 147, 66, 66, 66, 66, 66, 61, 31, 61, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 198, 147, 147, 147, 120, 120, 66, 66, 66, 66, 66, 66, 66, 31, 31, 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: 736 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: REAL300025241443 none CCN1C=NN=C1C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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, 8, 1, 8, 8, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 18, 26, 26, 26, 26, 26, 30, 30, 61, 93, 198, 198, 198, 198, 198, 3, 3, 3, 3, 3, 1, 7, 7, 7, 18, 18, 26, 26, 26, 26, 26, 26, 26, 61, 61, 198] 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: 479 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241443 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241443 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241443/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241443 Building REAL300025241444 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241444' /scratch/stefan/7787021/working/building/REAL300025241444 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241444 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241444/0 /scratch/stefan/7787021/working/building/REAL300025241444 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/314 `/scratch/stefan/7787021/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(C2CCC2)CC1) `REAL300025241444.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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: REAL300025241444 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(C2CCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', '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', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 97, 71, 71, 71, 71, 71, 58, 27, 58, 13, 1, 1, 1, 1, 1, 1, 1, 112, 163, 163, 171, 201, 201, 201, 171, 171, 112, 112, 112, 97, 97, 71, 71, 71, 71, 71, 71, 71, 27, 27, 1, 201, 201, 201, 201, 201, 201, 201, 171, 171, 171, 171] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 744 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.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: REAL300025241444 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(C2CCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', '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', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 11, 17, 21, 21, 21, 21, 21, 28, 28, 63, 104, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 8, 8, 11, 11, 11, 17, 17, 21, 21, 21, 21, 21, 21, 21, 63, 63, 201, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 201 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 49, 50, 51, 52]) total number of confs: 506 number of broken/clashed sets: 8 ./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: REAL300025241444 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(C2CCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', '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', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 10, 13, 13, 13, 13, 13, 19, 19, 48, 82, 171, 171, 171, 171, 171, 1, 3, 1, 1, 8, 8, 8, 1, 1, 7, 7, 7, 10, 10, 13, 13, 13, 13, 13, 13, 13, 48, 48, 171, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1] 201 rigid atoms, others: [50, 49, 18, 51, 20, 21, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 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: 410 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: REAL300025241444 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(C2CCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', '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', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 26, 71, 71, 71, 71, 71, 6, 12, 12, 13, 21, 21, 21, 13, 13, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 71, 21, 21, 21, 21, 21, 21, 21, 13, 13, 13, 13] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 204 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241444 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241444 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241444/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241444 Building REAL300025241445 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241445' /scratch/stefan/7787021/working/building/REAL300025241445 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241445 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241445/0 /scratch/stefan/7787021/working/building/REAL300025241445 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/315 `/scratch/stefan/7787021/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@@H]1CC[C@@H]2C[C@@H]21) `REAL300025241445.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241445 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@@H]1CC[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 129, 87, 87, 87, 87, 87, 65, 29, 65, 12, 1, 1, 1, 1, 1, 1, 1, 181, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 181, 181, 181, 129, 129, 87, 87, 87, 87, 87, 87, 87, 29, 29, 1, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [43, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 749 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: REAL300025241445 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@@H]1CC[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 9, 13, 23, 23, 23, 23, 23, 30, 30, 72, 116, 201, 201, 201, 201, 201, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 13, 23, 23, 23, 23, 23, 23, 23, 72, 72, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 49, 18, 20, 21, 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, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 533 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: REAL300025241445 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@@H]1CC[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 24, 87, 87, 87, 87, 87, 11, 21, 21, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 13, 13, 87, 23, 23, 23, 23, 23, 23] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 40, 39, 34, 8, 35, 36, 38, 37] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241445 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241445 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241445/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241445 Building REAL300025241446 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241446' /scratch/stefan/7787021/working/building/REAL300025241446 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241446 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241446/0 /scratch/stefan/7787021/working/building/REAL300025241446 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/316 `/scratch/stefan/7787021/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)COC1COC1) `REAL300025241446.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241446 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)COC1COC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'O.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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 30, 30, 30, 30, 30, 30, 18, 30, 11, 1, 1, 1, 1, 1, 1, 1, 52, 77, 77, 111, 145, 201, 201, 201, 52, 52, 52, 42, 42, 30, 30, 30, 30, 30, 30, 30, 18, 18, 1, 111, 111, 201, 201, 201, 201, 201] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 738 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: REAL300025241446 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)COC1COC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'O.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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 24, 32, 32, 32, 32, 32, 32, 32, 32, 56, 98, 201, 201, 201, 201, 201, 10, 17, 5, 1, 1, 1, 1, 1, 24, 24, 24, 32, 32, 32, 32, 32, 32, 32, 32, 32, 56, 56, 201, 10, 10, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 47, 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, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 511 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: REAL300025241446 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)COC1COC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'O.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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 30, 30, 30, 30, 30, 4, 8, 8, 14, 18, 32, 32, 32, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 30, 14, 14, 32, 32, 32, 32, 32] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241446 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241446 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241446/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241446 Building REAL300025241447 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241447' /scratch/stefan/7787021/working/building/REAL300025241447 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241447 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241447/0 /scratch/stefan/7787021/working/building/REAL300025241447 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/317 `/scratch/stefan/7787021/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@]2(C(=O)N(C)CC3CCCN3C(=O)CSC3=NNC(=O)[N-]3)C[C@H]12) `REAL300025241447.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241447 none C[C@@H]1C[C@]2(C(=O)N(C)CC3CCCN3C(=O)CSC3=NNC(=O)[N-]3)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 5, 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, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 10, 22, 4, 10, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 27, 87, 87, 87, 87, 87, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 87, 23, 23] 201 rigid atoms, others: [43, 38, 39, 40, 9, 10, 11, 12, 13, 14, 44, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 48, 49]) total number of confs: 214 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: REAL300025241447 none C[C@@H]1C[C@]2(C(=O)N(C)CC3CCCN3C(=O)CSC3=NNC(=O)[N-]3)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 5, 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, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 162, 196, 130, 162, 87, 87, 87, 87, 87, 69, 32, 69, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 162, 162, 162, 130, 130, 87, 87, 87, 87, 87, 87, 87, 32, 32, 1, 201, 201] 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]) total number of confs: 742 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: REAL300025241447 none C[C@@H]1C[C@]2(C(=O)N(C)CC3CCCN3C(=O)CSC3=NNC(=O)[N-]3)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 5, 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, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 4, 4, 8, 8, 13, 23, 23, 23, 23, 23, 30, 30, 64, 102, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 8, 8, 8, 13, 13, 23, 23, 23, 23, 23, 23, 23, 64, 64, 201, 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: 509 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241447 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241447 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241447/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241447 Building REAL300025241448 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241448' /scratch/stefan/7787021/working/building/REAL300025241448 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241448 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241448/0 /scratch/stefan/7787021/working/building/REAL300025241448 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/318 `/scratch/stefan/7787021/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241448.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241448 none CNC(=O)CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 4, 7, 6, 7, 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: [201, 201, 197, 201, 122, 110, 122, 94, 110, 49, 49, 49, 49, 49, 49, 29, 49, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 197, 197, 110, 110, 110, 94, 94, 49, 49, 49, 49, 49, 49, 49, 29, 29, 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: 887 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: REAL300025241448 none CNC(=O)CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 4, 7, 6, 7, 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: [57, 57, 26, 57, 10, 6, 10, 3, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 49, 49, 49, 49, 49, 57, 57, 57, 57, 26, 26, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 49] 201 rigid atoms, others: [36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241448 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241448 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241448/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241448 Building REAL300025241449 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241449' /scratch/stefan/7787021/working/building/REAL300025241449 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241449 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241449/0 /scratch/stefan/7787021/working/building/REAL300025241449 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/319 `/scratch/stefan/7787021/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1COC1)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241449.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241449 none CC(OC1COC1)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 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: [13, 6, 13, 29, 55, 55, 55, 5, 6, 4, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 12, 55, 55, 55, 55, 55, 13, 13, 13, 13, 55, 55, 55, 55, 55, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 55] 201 rigid atoms, others: [45, 43, 41, 42, 11, 12, 13, 14, 15, 16, 17, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50]) total number of confs: 240 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: REAL300025241449 none CC(OC1COC1)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 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: [157, 111, 157, 193, 201, 201, 201, 104, 111, 90, 104, 55, 55, 55, 55, 55, 55, 30, 55, 13, 1, 1, 1, 1, 1, 1, 1, 157, 157, 157, 157, 201, 201, 201, 201, 201, 104, 104, 104, 90, 90, 55, 55, 55, 55, 55, 55, 55, 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: 825 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: REAL300025241449 none CC(OC1COC1)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 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: [13, 6, 1, 1, 1, 1, 1, 13, 21, 21, 24, 24, 42, 55, 55, 55, 55, 55, 55, 55, 87, 129, 201, 201, 201, 201, 201, 13, 13, 13, 13, 1, 1, 1, 1, 1, 24, 24, 24, 42, 42, 55, 55, 55, 55, 55, 55, 55, 87, 87, 201] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 34, 35, 31] set([0, 1, 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: 607 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241449 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241449 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241449/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241449 Building REAL300025241450 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241450' /scratch/stefan/7787021/working/building/REAL300025241450 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241450 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241450/0 /scratch/stefan/7787021/working/building/REAL300025241450 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/320 `/scratch/stefan/7787021/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CCC(=O)N1C) `REAL300025241450.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241450 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 138, 85, 85, 85, 85, 85, 65, 30, 65, 13, 1, 1, 1, 1, 1, 1, 1, 172, 194, 194, 201, 201, 201, 201, 201, 201, 172, 172, 172, 138, 138, 85, 85, 85, 85, 85, 85, 85, 30, 30, 1, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 758 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: REAL300025241450 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 23, 29, 29, 65, 107, 201, 201, 201, 201, 201, 1, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 18, 18, 23, 23, 23, 23, 23, 23, 23, 65, 65, 201, 1, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [42, 43, 44, 45, 46, 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, 47, 48, 49]) total number of confs: 513 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: REAL300025241450 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 24, 85, 85, 85, 85, 85, 12, 20, 20, 23, 23, 23, 23, 23, 23, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 13, 13, 85, 23, 23, 23, 23, 23, 23, 23, 23] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 210 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241450 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241450 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241450/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241450 Building REAL300025241451 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241451' /scratch/stefan/7787021/working/building/REAL300025241451 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241451 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241451/0 /scratch/stefan/7787021/working/building/REAL300025241451 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/321 `/scratch/stefan/7787021/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CN(CC(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025241451.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241451 none CCC1CN(CC(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 21, 11, 10, 11, 5, 10, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 43, 43, 43, 43, 43, 32, 43, 43, 43, 43, 43, 32, 32, 32, 21, 21, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 43, 32, 32] 201 rigid atoms, others: [16, 45, 43, 44, 10, 11, 12, 13, 14, 15, 48, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 49, 50, 51, 52, 53]) total number of confs: 246 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: REAL300025241451 none CCC1CN(CC(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 191, 123, 121, 123, 77, 121, 43, 43, 43, 43, 43, 36, 31, 36, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 191, 191, 121, 121, 121, 77, 77, 43, 43, 43, 43, 43, 43, 43, 31, 31, 1, 201, 201] 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, 52, 53]) total number of confs: 821 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: REAL300025241451 none CCC1CN(CC(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 6, 9, 9, 11, 11, 26, 32, 32, 32, 32, 32, 50, 50, 81, 106, 201, 201, 201, 201, 201, 1, 3, 3, 3, 3, 3, 1, 1, 1, 6, 6, 11, 11, 11, 26, 26, 32, 32, 32, 32, 32, 32, 32, 81, 81, 201, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 34, 52, 53, 26] set([0, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 582 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241451 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241451/1 /scratch/stefan/7787021/working/building/REAL300025241451 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/322 `/scratch/stefan/7787021/working/3D/322' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1C[NH+](CC(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025241451.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241451/1/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: REAL300025241451 none CCC1C[NH+](CC(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 5, 9, 4, 3, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 8, 11, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 9, 9] 15 rigid atoms, others: [48, 11, 17, 47, 44, 43, 12, 13, 14, 45, 16, 49, 46, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 50, 51, 52, 53, 54]) total number of confs: 63 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: REAL300025241451 none CCC1C[NH+](CC(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 12, 15, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 12, 12, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 1, 15, 15] 15 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, 53, 54]) total number of confs: 41 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: REAL300025241451 none CCC1C[NH+](CC(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 10, 10, 11, 13, 15, 15, 15, 15, 15, 1, 3, 3, 3, 3, 3, 1, 1, 1, 5, 5, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 11, 11, 15, 1, 1] 15 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 34, 35, 53, 54, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241451 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241451 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241451/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241451/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241451 Building REAL300025241452 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241452' /scratch/stefan/7787021/working/building/REAL300025241452 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241452 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241452/0 /scratch/stefan/7787021/working/building/REAL300025241452 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/323 `/scratch/stefan/7787021/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN(C)C=C1C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241452.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241452 none CC1=CN(C)C=C1C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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 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, 37, 17, 6, 17, 4, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 14, 49, 49, 49, 49, 49, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 49] 201 rigid atoms, others: [45, 43, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49]) total number of confs: 158 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: REAL300025241452 none CC1=CN(C)C=C1C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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 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, 149, 105, 149, 88, 105, 49, 49, 49, 49, 49, 47, 28, 47, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 105, 105, 105, 88, 88, 49, 49, 49, 49, 49, 49, 49, 28, 28, 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: 694 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: REAL300025241452 none CC1=CN(C)C=C1C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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 201 conformations 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, 14, 14, 20, 37, 37, 37, 37, 37, 39, 39, 73, 113, 201, 201, 201, 201, 201, 2, 2, 2, 1, 2, 2, 2, 1, 14, 14, 14, 20, 20, 37, 37, 37, 37, 37, 37, 37, 73, 73, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 543 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241452 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241452 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241452/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241452 Building REAL300025241453 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241453' /scratch/stefan/7787021/working/building/REAL300025241453 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241453 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241453/0 /scratch/stefan/7787021/working/building/REAL300025241453 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/324 `/scratch/stefan/7787021/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC=CCC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241453.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241453 none C=CC=CCC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'C.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'] dock atom type numbers: [1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 156, 72, 72, 72, 63, 72, 39, 39, 39, 39, 39, 39, 29, 39, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 156, 156, 72, 72, 72, 63, 63, 39, 39, 39, 39, 39, 39, 39, 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: 886 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: REAL300025241453 none C=CC=CCC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'C.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'] dock atom type numbers: [1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 4, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 39, 39, 39, 39, 39, 53, 53, 53, 53, 53, 19, 19, 4, 4, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 39] 201 rigid atoms, others: [43, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241453 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241453 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241453/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241453 Building REAL300025241454 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241454' /scratch/stefan/7787021/working/building/REAL300025241454 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241454 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241454/0 /scratch/stefan/7787021/working/building/REAL300025241454 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/325 `/scratch/stefan/7787021/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)CCC1) `REAL300025241454.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241454 none C#CC1(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)CCC1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens 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, 14, 7, 14, 4, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 24, 84, 84, 84, 84, 84, 22, 22, 22, 22, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 13, 13, 84, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 220 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: REAL300025241454 none C#CC1(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)CCC1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens need 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, 134, 164, 122, 134, 84, 84, 84, 84, 84, 67, 31, 67, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 134, 134, 134, 122, 122, 84, 84, 84, 84, 84, 84, 84, 31, 31, 1, 201, 201, 201, 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]) total number of confs: 783 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: REAL300025241454 none C#CC1(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)CCC1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations 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, 7, 7, 14, 22, 22, 22, 22, 22, 31, 31, 65, 112, 201, 201, 201, 201, 201, 1, 1, 1, 1, 7, 7, 7, 14, 14, 22, 22, 22, 22, 22, 22, 22, 65, 65, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 42, 43, 44, 45, 46, 47, 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]) total number of confs: 508 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241454 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241454 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241454/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241454 Building REAL300025241455 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241455' /scratch/stefan/7787021/working/building/REAL300025241455 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300025241455 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241455/0 /scratch/stefan/7787021/working/building/REAL300025241455 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/326 `/scratch/stefan/7787021/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@@H]1CCC[N@@H+]1C) `REAL300025241455.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241455 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@@H]1CCC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'H', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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] 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: [157, 141, 135, 135, 135, 135, 135, 106, 35, 106, 12, 1, 1, 1, 1, 1, 1, 1, 157, 163, 163, 163, 163, 163, 163, 163, 163, 163, 157, 157, 157, 141, 141, 135, 135, 135, 135, 135, 135, 135, 35, 35, 1, 163, 163, 163, 163, 163, 163, 163, 163, 163] 163 rigid atoms, others: [42, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 495 number of broken/clashed sets: 128 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241455 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@@H]1CCC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'H', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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] 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: [6, 3, 6, 9, 10, 10, 10, 10, 10, 16, 16, 63, 102, 163, 163, 163, 163, 163, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 10, 10, 10, 10, 10, 10, 10, 63, 63, 163, 1, 1, 1, 1, 1, 1, 2, 2, 2] 163 rigid atoms, others: [43, 44, 45, 46, 47, 48, 18, 20, 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, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 418 number of broken/clashed sets: 128 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241455 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@@H]1CCC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'H', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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] 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: [6, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 18, 40, 135, 135, 135, 135, 135, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 18, 18, 135, 10, 10, 10, 10, 10, 10, 10, 10, 10] 163 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 39, 34, 35, 36, 38, 37] 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 252 number of broken/clashed sets: 128 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241455 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241455/1 /scratch/stefan/7787021/working/building/REAL300025241455 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/327 `/scratch/stefan/7787021/working/3D/327' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@@H]1CCC[N@H+]1C) `REAL300025241455.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241455/1/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: REAL300025241455 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@@H]1CCC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'H', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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] 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: [107, 102, 97, 97, 97, 97, 97, 82, 32, 82, 12, 1, 1, 1, 1, 1, 1, 1, 107, 109, 109, 109, 109, 109, 109, 109, 109, 109, 107, 107, 107, 102, 102, 97, 97, 97, 97, 97, 97, 97, 32, 32, 1, 109, 109, 109, 109, 109, 109, 109, 109, 109] 109 rigid atoms, others: [42, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 345 number of broken/clashed sets: 68 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241455 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@@H]1CCC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'H', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 11, 11, 32, 58, 109, 109, 109, 109, 109, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 32, 32, 109, 1, 1, 1, 1, 1, 1, 2, 2, 2] 109 rigid atoms, others: [43, 44, 45, 46, 47, 48, 18, 20, 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, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 259 number of broken/clashed sets: 68 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241455 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@@H]1CCC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'H', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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] 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: [4, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 35, 97, 97, 97, 97, 97, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 19, 19, 97, 7, 7, 7, 7, 7, 7, 7, 7, 7] 109 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 39, 34, 35, 36, 38, 37] 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 195 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241455 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `2' /scratch/stefan/7787021/working/building/REAL300025241455/2 /scratch/stefan/7787021/working/building/REAL300025241455 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 2 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/328 `/scratch/stefan/7787021/working/3D/328' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@@H]1CCCN1C) `REAL300025241455.mol2' -> `2.mol2' `temp.mol2' -> `REAL300025241455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241455/2/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: REAL300025241455 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 134, 88, 88, 88, 88, 88, 69, 32, 69, 12, 1, 1, 1, 1, 1, 1, 1, 173, 191, 191, 201, 201, 201, 201, 201, 201, 173, 173, 173, 134, 134, 88, 88, 88, 88, 88, 88, 88, 32, 32, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 771 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: REAL300025241455 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 11, 19, 27, 27, 27, 27, 27, 34, 34, 78, 121, 201, 201, 201, 201, 201, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 19, 19, 27, 27, 27, 27, 27, 27, 27, 78, 78, 201, 1, 1, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [42, 43, 44, 45, 46, 47, 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, 48, 49, 50]) total number of confs: 553 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: REAL300025241455 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 24, 88, 88, 88, 88, 88, 12, 21, 21, 27, 27, 27, 27, 27, 27, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 88, 27, 27, 27, 27, 27, 27, 27, 27, 27] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 223 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241455 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241455 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241455/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241455/1.* 2: /scratch/stefan/7787021/working/building/REAL300025241455/2.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241455 Building REAL300025241456 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241456' /scratch/stefan/7787021/working/building/REAL300025241456 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241456 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241456/0 /scratch/stefan/7787021/working/building/REAL300025241456 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/329 `/scratch/stefan/7787021/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC=CC(O)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241456.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241456 none CCCC=CC(O)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 12, 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, 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, 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, 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, 107, 107, 106, 95, 106, 95, 95, 75, 95, 47, 47, 47, 47, 47, 43, 37, 43, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 107, 107, 106, 318, 95, 95, 95, 75, 75, 47, 47, 47, 47, 47, 47, 47, 37, 37, 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: 1329 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: REAL300025241456 none CCCC=CC(O)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 12, 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, 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, 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, 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, 11, 11, 9, 7, 9, 7, 7, 4, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 20, 47, 47, 47, 47, 47, 20, 20, 20, 20, 20, 20, 20, 11, 11, 9, 27, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 47] 603 rigid atoms, others: [48, 11, 17, 47, 44, 43, 12, 13, 14, 45, 16, 49, 46, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 50, 51, 52]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241456 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241456 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241456/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241456 Building REAL300025241457 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241457' /scratch/stefan/7787021/working/building/REAL300025241457 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241457 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241457/0 /scratch/stefan/7787021/working/building/REAL300025241457 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/330 `/scratch/stefan/7787021/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CC=CCO1) `REAL300025241457.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241457 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CC=CCO1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 125, 83, 83, 83, 83, 83, 64, 30, 64, 13, 1, 1, 1, 1, 1, 1, 1, 156, 201, 201, 201, 201, 201, 201, 201, 156, 156, 156, 125, 125, 83, 83, 83, 83, 83, 83, 83, 30, 30, 1, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 710 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: REAL300025241457 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CC=CCO1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 12, 17, 27, 27, 27, 27, 27, 34, 34, 67, 109, 201, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 17, 17, 27, 27, 27, 27, 27, 27, 27, 67, 67, 201, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 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: 534 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: REAL300025241457 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CC=CCO1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 25, 83, 83, 83, 83, 83, 8, 20, 20, 27, 27, 27, 27, 27, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 83, 27, 27, 27, 27, 27, 27, 27] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 224 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241457 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241457 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241457/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241457 Building REAL300025241458 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241458' /scratch/stefan/7787021/working/building/REAL300025241458 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241458 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241458/0 /scratch/stefan/7787021/working/building/REAL300025241458 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/331 `/scratch/stefan/7787021/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C(C)(C)CCCO) `REAL300025241458.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241458 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C(C)(C)CCCO NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 93, 63, 63, 63, 63, 63, 54, 26, 54, 13, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 147, 147, 147, 201, 201, 201, 103, 103, 103, 93, 93, 63, 63, 63, 63, 63, 63, 63, 26, 26, 1, 147, 147, 147, 147, 147, 147, 201, 201, 201, 201, 201, 201, 603] 603 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 1551 number of broken/clashed sets: 603 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241458 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C(C)(C)CCCO NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 22, 63, 63, 63, 63, 63, 6, 6, 6, 9, 9, 9, 17, 17, 36, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 63, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 36, 36, 108] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 385 number of broken/clashed sets: 603 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241458 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241458 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241458/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241458 Building REAL300025241459 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241459' /scratch/stefan/7787021/working/building/REAL300025241459 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241459 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241459/0 /scratch/stefan/7787021/working/building/REAL300025241459 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/332 `/scratch/stefan/7787021/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CCOC1CC1) `REAL300025241459.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241459 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CCOC1CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 75, 46, 46, 46, 46, 46, 46, 30, 46, 13, 1, 1, 1, 1, 1, 1, 1, 93, 141, 141, 141, 141, 193, 201, 201, 93, 93, 93, 75, 75, 46, 46, 46, 46, 46, 46, 46, 30, 30, 1, 141, 141, 141, 141, 201, 201, 201, 201, 201] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 673 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: REAL300025241459 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CCOC1CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 50, 50, 50, 50, 50, 50, 50, 72, 114, 201, 201, 201, 201, 201, 16, 22, 16, 6, 1, 1, 1, 1, 31, 31, 31, 45, 45, 50, 50, 50, 50, 50, 50, 50, 72, 72, 201, 16, 16, 16, 16, 1, 1, 1, 1, 1] 201 rigid atoms, others: [45, 46, 47, 48, 49, 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, 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: 567 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: REAL300025241459 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CCOC1CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 46, 46, 46, 46, 46, 6, 11, 11, 11, 11, 26, 50, 50, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 46, 11, 11, 11, 11, 50, 50, 50, 50, 50] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241459 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241459 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241459/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241459 Building REAL300025241460 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241460' /scratch/stefan/7787021/working/building/REAL300025241460 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241460 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241460/0 /scratch/stefan/7787021/working/building/REAL300025241460 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/333 `/scratch/stefan/7787021/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CCCCCO) `REAL300025241460.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241460 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CCCCCO NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [152, 98, 55, 55, 55, 55, 55, 50, 41, 50, 13, 1, 1, 1, 1, 1, 1, 1, 152, 191, 191, 191, 200, 201, 201, 201, 152, 152, 152, 98, 98, 55, 55, 55, 55, 55, 55, 55, 41, 41, 1, 191, 191, 200, 200, 201, 201, 201, 201, 201, 201, 603] 603 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 1395 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: REAL300025241460 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CCCCCO NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 20, 55, 55, 55, 55, 55, 10, 17, 17, 17, 18, 19, 19, 31, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 55, 17, 17, 18, 18, 19, 19, 19, 19, 31, 31, 93] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241460 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241460 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241460/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241460 Building REAL300025241461 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241461' /scratch/stefan/7787021/working/building/REAL300025241461 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241461 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241461/0 /scratch/stefan/7787021/working/building/REAL300025241461 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/334 `/scratch/stefan/7787021/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CSC=N1) `REAL300025241461.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241461 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CSC=N1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 110, 74, 74, 74, 74, 74, 63, 31, 63, 13, 1, 1, 1, 1, 1, 1, 1, 136, 200, 200, 201, 201, 201, 201, 136, 136, 136, 110, 110, 74, 74, 74, 74, 74, 74, 74, 31, 31, 1, 201, 201] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 755 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: REAL300025241461 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CSC=N1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 17, 26, 26, 26, 26, 26, 30, 30, 64, 105, 201, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 10, 10, 10, 17, 17, 26, 26, 26, 26, 26, 26, 26, 64, 64, 201, 1, 1] 201 rigid atoms, others: [40, 41, 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: 517 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: REAL300025241461 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CSC=N1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 4, 14, 26, 74, 74, 74, 74, 74, 9, 22, 22, 26, 26, 26, 26, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 74, 26, 26] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 204 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241461 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241461 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241461/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241461 Building REAL300025241462 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241462' /scratch/stefan/7787021/working/building/REAL300025241462 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241462 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241462/0 /scratch/stefan/7787021/working/building/REAL300025241462 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/335 `/scratch/stefan/7787021/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C[NH+]1CCCCC1) `REAL300025241462.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241462 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C[NH+]1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 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, 7] 0 hydrogens 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, 134, 123, 123, 123, 123, 123, 93, 32, 93, 13, 1, 1, 1, 1, 1, 1, 1, 138, 149, 149, 156, 201, 201, 201, 201, 201, 201, 138, 138, 138, 134, 134, 123, 123, 123, 123, 123, 123, 123, 32, 32, 1, 156, 156, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [42, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 677 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: REAL300025241462 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C[NH+]1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 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, 7] 0 hydrogens 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, 8, 16, 17, 17, 17, 17, 17, 17, 26, 26, 78, 131, 201, 201, 201, 201, 201, 4, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 17, 17, 17, 17, 17, 17, 17, 17, 17, 78, 78, 201, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [54, 45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 27, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 513 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: REAL300025241462 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C[NH+]1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 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, 7] 0 hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 20, 44, 123, 123, 123, 123, 123, 5, 7, 7, 12, 17, 17, 17, 17, 17, 17, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 20, 20, 123, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 39, 34, 35, 36, 38, 37] 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 278 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241462 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241462/1 /scratch/stefan/7787021/working/building/REAL300025241462 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/336 `/scratch/stefan/7787021/working/3D/336' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CN1CCCCC1) `REAL300025241462.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241462/1/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: REAL300025241462 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CN1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 53, 32, 32, 32, 32, 32, 32, 23, 32, 12, 1, 1, 1, 1, 1, 1, 1, 94, 149, 149, 189, 201, 201, 201, 201, 201, 94, 94, 94, 53, 53, 32, 32, 32, 32, 32, 32, 32, 23, 23, 1, 189, 189, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 740 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: REAL300025241462 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CN1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 25, 30, 30, 30, 30, 30, 30, 30, 52, 94, 201, 201, 201, 201, 201, 5, 11, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 25, 25, 30, 30, 30, 30, 30, 30, 30, 52, 52, 201, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [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: 490 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: REAL300025241462 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CN1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 2, 2, 6, 10, 32, 32, 32, 32, 32, 9, 17, 17, 24, 30, 30, 30, 30, 30, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 32, 24, 24, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241462 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241462 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241462/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241462/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241462 Building REAL300025241463 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241463' /scratch/stefan/7787021/working/building/REAL300025241463 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241463 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241463/0 /scratch/stefan/7787021/working/building/REAL300025241463 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/337 `/scratch/stefan/7787021/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(CO)CCC1) `REAL300025241463.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241463 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(CO)CCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [137, 120, 86, 86, 86, 86, 86, 81, 30, 81, 13, 1, 1, 1, 1, 1, 1, 1, 137, 201, 201, 201, 201, 201, 201, 201, 137, 137, 137, 120, 120, 86, 86, 86, 86, 86, 86, 86, 30, 30, 1, 201, 201, 603, 201, 201, 201, 201, 201, 201] 603 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 1323 number of broken/clashed sets: 132 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241463 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(CO)CCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 4, 5, 9, 13, 13, 13, 13, 13, 15, 15, 42, 80, 201, 201, 201, 201, 201, 1, 4, 1, 1, 8, 1, 1, 1, 5, 5, 5, 9, 9, 13, 13, 13, 13, 13, 13, 13, 42, 42, 201, 8, 8, 24, 1, 1, 1, 1, 1, 1] 603 rigid atoms, others: [44, 45, 46, 47, 48, 49, 18, 20, 21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 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: 132 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241463 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(CO)CCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 25, 86, 86, 86, 86, 86, 7, 13, 13, 13, 34, 13, 13, 13, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 86, 34, 34, 102, 13, 13, 13, 13, 13, 13] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 377 number of broken/clashed sets: 132 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241463 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241463 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241463/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241463 Building REAL300025241464 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241464' /scratch/stefan/7787021/working/building/REAL300025241464 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241464 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241464/0 /scratch/stefan/7787021/working/building/REAL300025241464 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/338 `/scratch/stefan/7787021/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CCCCC1O) `REAL300025241464.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241464 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CCCCC1O NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [146, 115, 79, 79, 79, 79, 79, 62, 27, 62, 12, 1, 1, 1, 1, 1, 1, 1, 146, 187, 187, 201, 201, 201, 201, 201, 201, 146, 146, 146, 115, 115, 79, 79, 79, 79, 79, 79, 79, 27, 27, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 603] 603 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 1342 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: REAL300025241464 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CCCCC1O NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 12, 16, 22, 22, 22, 22, 22, 28, 28, 61, 100, 201, 201, 201, 201, 201, 1, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 16, 16, 22, 22, 22, 22, 22, 22, 22, 61, 61, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3] 603 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52]) total number of confs: 498 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: REAL300025241464 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CCCCC1O NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 23, 79, 79, 79, 79, 79, 10, 19, 19, 22, 22, 22, 22, 22, 22, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 79, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 66] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 267 number of broken/clashed sets: 165 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241464 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241464 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241464/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241464 Building REAL300025241465 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241465' /scratch/stefan/7787021/working/building/REAL300025241465 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241465 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241465/0 /scratch/stefan/7787021/working/building/REAL300025241465 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/339 `/scratch/stefan/7787021/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CC1=NC=CN1C) `REAL300025241465.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241465 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CC1=NC=CN1C NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 56, 36, 36, 36, 36, 36, 35, 25, 35, 12, 1, 1, 1, 1, 1, 1, 1, 80, 139, 139, 196, 201, 201, 201, 201, 201, 80, 80, 80, 56, 56, 36, 36, 36, 36, 36, 36, 36, 25, 25, 1, 196, 196, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 814 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241465 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CC1=NC=CN1C NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 32, 33, 33, 33, 33, 33, 33, 33, 56, 97, 201, 201, 201, 201, 201, 3, 11, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 32, 32, 33, 33, 33, 33, 33, 33, 33, 56, 56, 201, 3, 3, 1, 1, 2, 2, 2] 201 rigid atoms, others: [44, 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, 46, 47, 48]) total number of confs: 529 number of broken/clashed sets: 64 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241465 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CC1=NC=CN1C NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 9, 36, 36, 36, 36, 36, 7, 14, 14, 30, 33, 33, 33, 33, 33, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 36, 30, 30, 33, 33, 33, 33, 33] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 172 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241465 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241465 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241465/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241465 Building REAL300025241466 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241466' /scratch/stefan/7787021/working/building/REAL300025241466 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241466 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241466/0 /scratch/stefan/7787021/working/building/REAL300025241466 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/340 `/scratch/stefan/7787021/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC[N@@H+]1C) `REAL300025241466.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241466 none CC1C(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC[N@@H+]1C 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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 19, 30, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 16, 16, 30, 5, 5, 5, 5, 5, 5, 5] 30 rigid atoms, others: [11, 38, 7, 8, 9, 10, 39, 12, 13, 44, 40, 43, 41, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 90 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: REAL300025241466 none CC1C(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC[N@@H+]1C 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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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 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, 30, 30, 30, 30, 30, 30, 30, 28, 20, 28, 11, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 20, 20, 1, 30, 30, 30, 30, 30, 30, 30] 30 rigid atoms, others: [47, 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, 46, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 91 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: REAL300025241466 none CC1C(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC[N@@H+]1C 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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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 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, 4, 5, 5, 5, 5, 5, 5, 7, 7, 19, 21, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 30, 1, 1, 1, 1, 2, 2, 2] 30 rigid atoms, others: [0, 1, 2, 3, 32, 48, 49, 50, 51, 23, 24, 25, 26, 27, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 52, 53, 54]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241466 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241466/1 /scratch/stefan/7787021/working/building/REAL300025241466 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/341 `/scratch/stefan/7787021/working/3D/341' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC[N@H+]1C) `REAL300025241466.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241466/1/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: REAL300025241466 none CC1C(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC[N@H+]1C 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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 8, 4, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 42, 89, 89, 89, 89, 89, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 24, 24, 89, 10, 10, 10, 10, 10, 10, 10] 94 rigid atoms, others: [11, 38, 7, 8, 9, 10, 39, 12, 13, 44, 40, 43, 41, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 217 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: REAL300025241466 none CC1C(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC[N@H+]1C 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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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 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, 93, 94, 93, 93, 89, 89, 89, 89, 89, 78, 30, 78, 13, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 93, 93, 93, 93, 93, 89, 89, 89, 89, 89, 89, 89, 30, 30, 1, 94, 94, 94, 94, 94, 94, 94] 94 rigid atoms, others: [47, 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, 46, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 291 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: REAL300025241466 none CC1C(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC[N@H+]1C 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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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 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, 4, 4, 6, 6, 9, 10, 10, 10, 10, 10, 13, 13, 36, 58, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 6, 6, 6, 9, 9, 10, 10, 10, 10, 10, 10, 10, 36, 36, 94, 1, 1, 1, 1, 2, 2, 2] 94 rigid atoms, others: [0, 1, 2, 3, 32, 48, 49, 50, 51, 23, 24, 25, 26, 27, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 52, 53, 54]) total number of confs: 251 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241466 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241466 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241466/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241466/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241466 Building REAL300025241467 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241467' /scratch/stefan/7787021/working/building/REAL300025241467 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241467 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241467/0 /scratch/stefan/7787021/working/building/REAL300025241467 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/342 `/scratch/stefan/7787021/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CN=CC(=O)N1) `REAL300025241467.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241467 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CN=CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 8, 1, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 36, 36, 36, 36, 36, 35, 24, 35, 13, 1, 1, 1, 1, 1, 1, 1, 74, 133, 133, 201, 201, 201, 201, 201, 201, 74, 74, 74, 49, 49, 36, 36, 36, 36, 36, 36, 36, 24, 24, 1, 201, 201, 201] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 585 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: REAL300025241467 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CN=CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 8, 1, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 26, 30, 30, 30, 30, 30, 32, 32, 59, 98, 201, 201, 201, 201, 201, 1, 9, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 26, 26, 30, 30, 30, 30, 30, 30, 30, 59, 59, 201, 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: 534 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: REAL300025241467 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CN=CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 8, 1, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 10, 36, 36, 36, 36, 36, 7, 14, 14, 30, 30, 30, 30, 30, 30, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 36, 30, 30, 30] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44]) total number of confs: 123 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241467 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241467 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241467/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241467 Building REAL300025241468 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241468' /scratch/stefan/7787021/working/building/REAL300025241468 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241468 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241468/0 /scratch/stefan/7787021/working/building/REAL300025241468 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/343 `/scratch/stefan/7787021/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CNC(=O)S1) `REAL300025241468.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241468 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CNC(=O)S1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 8, 1, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 60, 43, 43, 43, 43, 43, 42, 26, 42, 13, 1, 1, 1, 1, 1, 1, 1, 87, 141, 141, 201, 201, 201, 201, 201, 87, 87, 87, 60, 60, 43, 43, 43, 43, 43, 43, 43, 26, 26, 1, 201, 201] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 624 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: REAL300025241468 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CNC(=O)S1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 8, 1, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 17, 27, 34, 34, 34, 34, 34, 35, 35, 59, 97, 201, 201, 201, 201, 201, 1, 10, 1, 1, 1, 1, 1, 1, 17, 17, 17, 27, 27, 34, 34, 34, 34, 34, 34, 34, 59, 59, 201, 1, 1] 201 rigid atoms, others: [41, 42, 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: 507 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: REAL300025241468 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CNC(=O)S1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 8, 1, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 12, 43, 43, 43, 43, 43, 10, 18, 18, 34, 34, 34, 34, 34, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 43, 34, 34] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241468 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241468 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241468/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241468 Building REAL300025241469 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241469' /scratch/stefan/7787021/working/building/REAL300025241469 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241469 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241469/0 /scratch/stefan/7787021/working/building/REAL300025241469 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/344 `/scratch/stefan/7787021/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CCC(N)=O) `REAL300025241469.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241469 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CCC(N)=O NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 28, 28, 28, 28, 28, 28, 22, 28, 10, 1, 1, 1, 1, 1, 1, 1, 78, 144, 144, 144, 193, 201, 201, 78, 78, 78, 48, 48, 28, 28, 28, 28, 28, 28, 28, 22, 22, 1, 144, 144, 193, 193, 201, 201] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 837 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: REAL300025241469 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CCC(N)=O NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 28, 28, 28, 28, 28, 7, 15, 15, 15, 24, 38, 38, 7, 7, 7, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 28, 15, 15, 24, 24, 38, 38] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241469 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241469 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241469/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241469 Building REAL300025241470 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241470' /scratch/stefan/7787021/working/building/REAL300025241470 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241470 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241470/0 /scratch/stefan/7787021/working/building/REAL300025241470 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/345 `/scratch/stefan/7787021/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC1) `REAL300025241470.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241470 none C=CCC1(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 11, 11, 6, 11, 4, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 17, 82, 82, 82, 82, 82, 11, 11, 34, 34, 34, 19, 19, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 82, 11, 11, 11, 11] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 248 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: REAL300025241470 none C=CCC1(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 200, 168, 200, 132, 168, 82, 82, 82, 82, 82, 82, 32, 82, 13, 1, 1, 1, 1, 1, 1, 1, 200, 200, 201, 201, 201, 201, 201, 168, 168, 168, 132, 132, 82, 82, 82, 82, 82, 82, 82, 32, 32, 1, 200, 200, 200, 200] 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: 791 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: REAL300025241470 none C=CCC1(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 3, 3, 5, 5, 7, 11, 11, 11, 11, 11, 11, 11, 42, 76, 200, 200, 200, 200, 200, 1, 1, 16, 16, 16, 7, 7, 5, 5, 5, 7, 7, 11, 11, 11, 11, 11, 11, 11, 42, 42, 200, 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: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241470 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241470 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241470/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241470 Building REAL300025241471 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241471' /scratch/stefan/7787021/working/building/REAL300025241471 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241471 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241471/0 /scratch/stefan/7787021/working/building/REAL300025241471 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/346 `/scratch/stefan/7787021/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)COC(F)F) `REAL300025241471.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241471 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)COC(F)F NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'O.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 57, 37, 37, 37, 37, 37, 37, 26, 37, 13, 1, 1, 1, 1, 1, 1, 1, 76, 121, 121, 155, 201, 201, 201, 76, 76, 76, 57, 57, 37, 37, 37, 37, 37, 37, 37, 26, 26, 1, 155, 155, 201] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 720 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: REAL300025241471 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)COC(F)F NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'O.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 37, 37, 37, 37, 37, 6, 12, 12, 20, 30, 39, 39, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 37, 20, 20, 39] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241471 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241471 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241471/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241471 Building REAL300025241472 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241472' /scratch/stefan/7787021/working/building/REAL300025241472 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241472 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241472/0 /scratch/stefan/7787021/working/building/REAL300025241472 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/347 `/scratch/stefan/7787021/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(C)CCC(=O)N1) `REAL300025241472.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241472 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(C)CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 122, 122, 122, 122, 122, 86, 32, 86, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 161, 161, 122, 122, 122, 122, 122, 122, 122, 32, 32, 1, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 714 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: REAL300025241472 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(C)CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 3, 6, 10, 10, 10, 10, 10, 25, 25, 73, 111, 201, 201, 201, 201, 201, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 10, 10, 10, 10, 10, 10, 10, 73, 73, 201, 2, 2, 2, 1, 1, 1, 1, 1] 201 rigid atoms, others: [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, 42, 43, 44]) total number of confs: 506 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: REAL300025241472 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(C)CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 44, 122, 122, 122, 122, 122, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 24, 24, 122, 10, 10, 10, 10, 10, 10, 10, 10] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 253 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241472 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241472 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241472/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241472 Building REAL300025241473 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241473' /scratch/stefan/7787021/working/building/REAL300025241473 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241473 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241473/0 /scratch/stefan/7787021/working/building/REAL300025241473 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/348 `/scratch/stefan/7787021/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241473.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241473 none COC(C)(C)CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 201, 201, 122, 112, 122, 85, 112, 58, 58, 58, 58, 58, 54, 28, 54, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 181, 181, 112, 112, 112, 85, 85, 58, 58, 58, 58, 58, 58, 58, 28, 28, 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: 894 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: REAL300025241473 none COC(C)(C)CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 22, 17, 22, 22, 10, 7, 10, 4, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 18, 58, 58, 58, 58, 58, 35, 35, 35, 22, 22, 22, 22, 22, 22, 17, 17, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 58] 201 rigid atoms, others: [16, 45, 43, 44, 10, 11, 12, 13, 14, 15, 48, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 49, 50, 51]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241473 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241473 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241473/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241473 Building REAL300025241474 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241474' /scratch/stefan/7787021/working/building/REAL300025241474 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241474 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241474/0 /scratch/stefan/7787021/working/building/REAL300025241474 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/349 `/scratch/stefan/7787021/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CCC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241474.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241474 none CC(O)CCC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 7, 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] 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, 179, 201, 171, 106, 91, 106, 76, 91, 48, 48, 48, 48, 48, 48, 29, 48, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 603, 179, 179, 171, 171, 91, 91, 91, 76, 76, 48, 48, 48, 48, 48, 48, 48, 29, 29, 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: 1501 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: REAL300025241474 none CC(O)CCC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 7, 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] 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, 26, 32, 22, 8, 6, 8, 3, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 48, 48, 48, 48, 48, 32, 32, 32, 32, 96, 26, 26, 22, 22, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 48] 603 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48]) total number of confs: 301 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241474 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241474 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241474/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241474 Building REAL300025241475 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241475' /scratch/stefan/7787021/working/building/REAL300025241475 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241475 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241475/0 /scratch/stefan/7787021/working/building/REAL300025241475 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/350 `/scratch/stefan/7787021/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(O)=CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241475.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 Warning: Using closest atom type 60 for atom 3 Warning: Using closest atom type 60 for atom 3 ('energy: ', 12.0) ('conf: ', 200) Warning: Using closest atom type 60 for atom 3 Warning: Using closest atom type 60 for atom 3 ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241475 none CCS(O)=CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'O.3', 'C.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', 'H'] dock atom type numbers: [5, 5, 14, 12, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 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: [201, 201, 201, 201, 178, 155, 178, 114, 155, 75, 75, 75, 75, 75, 75, 32, 75, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 155, 155, 155, 114, 114, 75, 75, 75, 75, 75, 75, 75, 32, 32, 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: 806 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: REAL300025241475 none CCS(O)=CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'O.3', 'C.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', 'H'] dock atom type numbers: [5, 5, 14, 12, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 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: [27, 17, 17, 17, 12, 7, 12, 4, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 14, 75, 75, 75, 75, 75, 27, 27, 27, 27, 27, 17, 17, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 75] 201 rigid atoms, others: [43, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241475 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241475 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241475/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241475 Building REAL300025241476 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241476' /scratch/stefan/7787021/working/building/REAL300025241476 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241476 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241476/0 /scratch/stefan/7787021/working/building/REAL300025241476 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/351 `/scratch/stefan/7787021/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CCC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241476.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241476 none CN(C)C(=O)CCC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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, 7] 0 hydrogens need 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, 196, 134, 111, 134, 93, 111, 56, 56, 56, 56, 56, 49, 27, 49, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 196, 196, 111, 111, 111, 93, 93, 56, 56, 56, 56, 56, 56, 56, 27, 27, 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: 831 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: REAL300025241476 none CN(C)C(=O)CCC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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, 7] 0 hydrogens 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, 39, 44, 32, 14, 8, 14, 3, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 17, 56, 56, 56, 56, 56, 44, 44, 44, 44, 44, 44, 39, 39, 32, 32, 8, 8, 8, 3, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 56] 201 rigid atoms, others: [48, 45, 43, 44, 42, 11, 12, 13, 14, 15, 16, 17, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 49, 50, 51]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241476 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241476 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241476/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241476 Building REAL300025241477 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241477' /scratch/stefan/7787021/working/building/REAL300025241477 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241477 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241477/0 /scratch/stefan/7787021/working/building/REAL300025241477 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/352 `/scratch/stefan/7787021/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC(C)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241477.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241477 none C#CCC(C)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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: [1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 123, 173, 115, 123, 96, 115, 65, 65, 65, 65, 65, 56, 30, 56, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 173, 173, 173, 173, 115, 115, 115, 96, 96, 65, 65, 65, 65, 65, 65, 65, 30, 30, 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: 929 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: REAL300025241477 none C#CCC(C)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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: [1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 10, 19, 7, 10, 4, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 20, 65, 65, 65, 65, 65, 32, 32, 32, 19, 19, 19, 19, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 65] 201 rigid atoms, others: [43, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241477 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241477 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241477/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241477 Building REAL300025241478 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241478' /scratch/stefan/7787021/working/building/REAL300025241478 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241478 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241478/0 /scratch/stefan/7787021/working/building/REAL300025241478 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/353 `/scratch/stefan/7787021/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCO)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241478.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241478 none CC(CCO)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 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: [189, 159, 189, 201, 201, 143, 159, 129, 143, 81, 81, 81, 81, 81, 70, 31, 70, 13, 1, 1, 1, 1, 1, 1, 1, 189, 189, 189, 189, 201, 201, 201, 201, 603, 143, 143, 143, 129, 129, 81, 81, 81, 81, 81, 81, 81, 31, 31, 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: 1477 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241478 none CC(CCO)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 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, 12, 19, 29, 41, 7, 12, 4, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 20, 81, 81, 81, 81, 81, 19, 19, 19, 19, 31, 31, 39, 41, 123, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 81] 603 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48]) total number of confs: 455 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241478 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241478 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241478/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241478 Building REAL300025241479 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241479' /scratch/stefan/7787021/working/building/REAL300025241479 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241479 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241479/0 /scratch/stefan/7787021/working/building/REAL300025241479 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/354 `/scratch/stefan/7787021/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C(F)=CC1CC1) `REAL300025241479.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241479 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C(F)=CC1CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'F', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 49, 31, 31, 31, 31, 31, 31, 23, 31, 12, 1, 1, 1, 1, 1, 1, 1, 66, 121, 121, 138, 138, 138, 201, 201, 66, 66, 66, 49, 49, 31, 31, 31, 31, 31, 31, 31, 23, 23, 1, 138, 201, 201, 201, 201, 201] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 745 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: REAL300025241479 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C(F)=CC1CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'F', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 41, 44, 44, 44, 44, 44, 44, 44, 69, 109, 201, 201, 201, 201, 201, 7, 18, 7, 7, 1, 1, 1, 1, 29, 29, 29, 41, 41, 44, 44, 44, 44, 44, 44, 44, 69, 69, 201, 7, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 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, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 572 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: REAL300025241479 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C(F)=CC1CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'F', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 6, 31, 31, 31, 31, 31, 7, 14, 14, 17, 17, 17, 44, 44, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 31, 17, 44, 44, 44, 44, 44] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241479 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241479 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241479/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241479 Building REAL300025241480 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241480' /scratch/stefan/7787021/working/building/REAL300025241480 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241480 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241480/0 /scratch/stefan/7787021/working/building/REAL300025241480 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/355 `/scratch/stefan/7787021/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CC1CC(F)C1) `REAL300025241480.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241480 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CC1CC(F)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.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, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 76, 48, 48, 48, 48, 48, 48, 29, 48, 13, 1, 1, 1, 1, 1, 1, 1, 105, 132, 132, 133, 201, 201, 201, 201, 105, 105, 105, 76, 76, 48, 48, 48, 48, 48, 48, 48, 29, 29, 1, 133, 133, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 801 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: REAL300025241480 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CC1CC(F)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.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, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 21, 28, 33, 33, 33, 33, 33, 33, 33, 60, 96, 201, 201, 201, 201, 201, 5, 14, 1, 1, 1, 1, 1, 1, 21, 21, 21, 28, 28, 33, 33, 33, 33, 33, 33, 33, 60, 60, 201, 5, 5, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 47, 48, 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: 506 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: REAL300025241480 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CC1CC(F)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.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, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 11, 48, 48, 48, 48, 48, 8, 14, 14, 17, 33, 33, 33, 33, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 48, 17, 17, 33, 33, 33, 33, 33, 33] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241480 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241480 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241480/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241480 Building REAL300025241481 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241481' /scratch/stefan/7787021/working/building/REAL300025241481 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241481 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241481/0 /scratch/stefan/7787021/working/building/REAL300025241481 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/356 `/scratch/stefan/7787021/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C(F)CC1CCC1) `REAL300025241481.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241481 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C(F)CC1CCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 70, 43, 43, 43, 43, 43, 42, 26, 42, 13, 1, 1, 1, 1, 1, 1, 1, 81, 129, 129, 129, 129, 129, 201, 201, 201, 81, 81, 81, 70, 70, 43, 43, 43, 43, 43, 43, 43, 26, 26, 1, 129, 129, 129, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 765 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: REAL300025241481 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C(F)CC1CCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 18, 24, 36, 36, 36, 36, 36, 38, 38, 70, 106, 201, 201, 201, 201, 201, 6, 12, 4, 6, 1, 1, 1, 1, 1, 18, 18, 18, 24, 24, 36, 36, 36, 36, 36, 36, 36, 70, 70, 201, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 22, 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, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 555 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: REAL300025241481 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C(F)CC1CCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 13, 43, 43, 43, 43, 43, 6, 12, 12, 12, 12, 19, 36, 36, 36, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 43, 12, 19, 19, 36, 36, 36, 36, 36, 36, 36] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241481 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241481 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241481/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241481 Building REAL300025241482 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241482' /scratch/stefan/7787021/working/building/REAL300025241482 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241482 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241482/0 /scratch/stefan/7787021/working/building/REAL300025241482 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/357 `/scratch/stefan/7787021/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@H](O)CF) `REAL300025241482.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241482 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@H](O)CF NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 12, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 88, 60, 60, 60, 60, 60, 60, 38, 60, 13, 1, 1, 1, 1, 1, 1, 1, 129, 183, 183, 201, 201, 201, 201, 129, 129, 129, 88, 88, 60, 60, 60, 60, 60, 60, 60, 38, 38, 1, 603, 201, 201] 603 rigid atoms, others: [39, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 1400 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: REAL300025241482 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)[C@H](O)CF NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 12, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 11, 60, 60, 60, 60, 60, 10, 20, 20, 25, 25, 25, 36, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 60, 75, 36, 36] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 299 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241482 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241482 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241482/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241482 Building REAL300025241483 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241483' /scratch/stefan/7787021/working/building/REAL300025241483 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241483 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241483/0 /scratch/stefan/7787021/working/building/REAL300025241483 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/358 `/scratch/stefan/7787021/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C)C=C(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025241483.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241483 none CCC1(C)C=C(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 11, 5, 11, 4, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 41, 41, 41, 41, 41, 32, 44, 44, 44, 44, 44, 32, 32, 32, 32, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 41, 32, 32] 201 rigid atoms, others: [45, 43, 41, 10, 11, 12, 13, 14, 15, 16, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 51, 52]) total number of confs: 193 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: REAL300025241483 none CCC1(C)C=C(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 110, 79, 110, 70, 79, 41, 41, 41, 41, 41, 41, 27, 41, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 79, 79, 70, 70, 41, 41, 41, 41, 41, 41, 41, 27, 27, 1, 201, 201] 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]) 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: REAL300025241483 none CCC1(C)C=C(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens 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, 12, 12, 18, 18, 27, 32, 32, 32, 32, 32, 32, 32, 51, 86, 201, 201, 201, 201, 201, 1, 3, 3, 3, 3, 3, 2, 2, 2, 1, 18, 18, 18, 27, 27, 32, 32, 32, 32, 32, 32, 32, 51, 51, 201, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 52, 26, 51] 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 467 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241483 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241483 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241483/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241483 Building REAL300025241484 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241484' /scratch/stefan/7787021/working/building/REAL300025241484 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241484 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241484/0 /scratch/stefan/7787021/working/building/REAL300025241484 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/359 `/scratch/stefan/7787021/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C)CC(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025241484.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241484 none CCC1(C)CC(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 6, 9, 4, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 46, 46, 46, 46, 46, 22, 36, 36, 36, 36, 36, 22, 22, 22, 22, 22, 22, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 46, 22, 22] 201 rigid atoms, others: [16, 45, 11, 44, 10, 43, 12, 13, 14, 15, 48, 49, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 50, 51, 52, 53, 54]) total number of confs: 213 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: REAL300025241484 none CCC1(C)CC(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 103, 131, 76, 103, 46, 46, 46, 46, 46, 46, 30, 46, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 103, 103, 76, 76, 46, 46, 46, 46, 46, 46, 46, 30, 30, 1, 201, 201] 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]) total number of confs: 745 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: REAL300025241484 none CCC1(C)CC(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 11, 11, 16, 22, 22, 22, 22, 22, 22, 22, 41, 78, 201, 201, 201, 201, 201, 1, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 11, 11, 11, 16, 16, 22, 22, 22, 22, 22, 22, 22, 41, 41, 201, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 53, 54, 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, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 439 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241484 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241484 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241484/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241484 Building REAL300025241485 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241485' /scratch/stefan/7787021/working/building/REAL300025241485 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241485 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241485/0 /scratch/stefan/7787021/working/building/REAL300025241485 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/360 `/scratch/stefan/7787021/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=NC(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)=N1) `REAL300025241485.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241485 none CCN1C=NC(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)=N1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 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, 7, 7, 7, 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: [43, 23, 23, 23, 23, 5, 5, 5, 4, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 42, 42, 42, 42, 42, 23, 43, 43, 43, 43, 43, 23, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 42] 201 rigid atoms, others: [43, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47]) total number of confs: 216 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: REAL300025241485 none CCN1C=NC(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)=N1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 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, 7, 7, 7, 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: [201, 152, 152, 152, 152, 82, 82, 82, 76, 82, 42, 42, 42, 42, 42, 42, 28, 42, 13, 1, 1, 1, 1, 1, 1, 1, 152, 201, 201, 201, 201, 201, 152, 82, 82, 82, 76, 76, 42, 42, 42, 42, 42, 42, 42, 28, 28, 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: 754 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: REAL300025241485 none CCN1C=NC(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)=N1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 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, 7, 7, 7, 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: [4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 19, 23, 23, 23, 23, 23, 23, 23, 40, 71, 152, 152, 152, 152, 152, 1, 4, 4, 4, 4, 4, 1, 10, 10, 10, 19, 19, 23, 23, 23, 23, 23, 23, 23, 40, 40, 152] 201 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: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241485 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241485 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241485/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241485 Building REAL300025241486 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241486' /scratch/stefan/7787021/working/building/REAL300025241486 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241486 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241486/0 /scratch/stefan/7787021/working/building/REAL300025241486 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/361 `/scratch/stefan/7787021/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)(O)CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241486.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241486 none CCCC(C)(O)CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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, 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, 159, 159, 159, 159, 142, 123, 142, 97, 123, 60, 60, 60, 60, 60, 54, 29, 54, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 159, 159, 159, 477, 159, 159, 123, 123, 123, 97, 97, 60, 60, 60, 60, 60, 60, 60, 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: 1392 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: REAL300025241486 none CCCC(C)(O)CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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, 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: [42, 42, 15, 14, 15, 15, 9, 7, 9, 4, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 17, 60, 60, 60, 60, 60, 42, 42, 42, 42, 42, 42, 42, 15, 15, 15, 45, 14, 14, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 60] 603 rigid atoms, others: [48, 17, 15, 11, 12, 13, 14, 45, 16, 49, 50, 51, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 52, 53, 54]) total number of confs: 314 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241486 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241486 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241486/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241486 Building REAL300025241487 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241487' /scratch/stefan/7787021/working/building/REAL300025241487 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241487 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241487/0 /scratch/stefan/7787021/working/building/REAL300025241487 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/362 `/scratch/stefan/7787021/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=NN=CN1C) `REAL300025241487.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241487 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=NN=CN1C NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 110, 66, 66, 66, 66, 66, 53, 30, 53, 13, 1, 1, 1, 1, 1, 1, 1, 147, 196, 196, 201, 201, 201, 201, 201, 147, 147, 147, 110, 110, 66, 66, 66, 66, 66, 66, 66, 30, 30, 1, 201, 201, 201, 201] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 751 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: REAL300025241487 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=NN=CN1C NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 13, 22, 27, 27, 27, 27, 27, 33, 33, 60, 104, 201, 201, 201, 201, 201, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 22, 22, 27, 27, 27, 27, 27, 27, 27, 60, 60, 201, 1, 2, 2, 2] 201 rigid atoms, others: [41, 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, 42, 43, 44]) total number of confs: 510 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: REAL300025241487 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=NN=CN1C NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 20, 66, 66, 66, 66, 66, 10, 19, 19, 27, 27, 27, 27, 27, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 66, 27, 27, 27, 27] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241487 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241487 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241487/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241487 Building REAL300025241488 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241488' /scratch/stefan/7787021/working/building/REAL300025241488 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241488 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241488/0 /scratch/stefan/7787021/working/building/REAL300025241488 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/363 `/scratch/stefan/7787021/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(CC)CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241488.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241488 none CCCC(CC)CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 152, 178, 178, 80, 74, 80, 49, 74, 30, 30, 30, 30, 30, 30, 18, 30, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 178, 178, 178, 178, 178, 178, 152, 152, 74, 74, 74, 49, 49, 30, 30, 30, 30, 30, 30, 30, 18, 18, 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: 931 number of broken/clashed sets: 74 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241488 none CCCC(CC)CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 23, 34, 42, 7, 6, 7, 3, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 6, 30, 30, 30, 30, 30, 47, 47, 47, 47, 47, 47, 47, 34, 42, 42, 42, 42, 42, 23, 23, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 30] 201 rigid atoms, others: [48, 17, 11, 12, 13, 14, 47, 16, 49, 50, 51, 52, 53, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 54, 55, 56]) total number of confs: 320 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241488 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241488 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241488/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241488 Building REAL300025241489 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241489' /scratch/stefan/7787021/working/building/REAL300025241489 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241489 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241489/0 /scratch/stefan/7787021/working/building/REAL300025241489 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/364 `/scratch/stefan/7787021/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CON=C1CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241489.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241489 none CC1=CON=C1CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.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'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 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: [36, 36, 36, 36, 36, 27, 10, 7, 10, 4, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 12, 49, 49, 49, 49, 49, 36, 36, 36, 36, 27, 27, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 49] 201 rigid atoms, others: [43, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47]) total number of confs: 191 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241489 none CC1=CON=C1CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.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'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 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: [201, 201, 201, 201, 201, 196, 114, 101, 114, 85, 101, 49, 49, 49, 49, 49, 49, 30, 49, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 196, 196, 101, 101, 101, 85, 85, 49, 49, 49, 49, 49, 49, 49, 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: 874 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: REAL300025241489 none CC1=CON=C1CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.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'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 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, 1, 1, 1, 6, 14, 14, 18, 18, 29, 36, 36, 36, 36, 36, 37, 37, 61, 108, 201, 201, 201, 201, 201, 2, 2, 2, 1, 6, 6, 18, 18, 18, 29, 29, 36, 36, 36, 36, 36, 36, 36, 61, 61, 201] 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: 529 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241489 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241489 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241489/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241489 Building REAL300025241490 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241490' /scratch/stefan/7787021/working/building/REAL300025241490 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241490 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241490/0 /scratch/stefan/7787021/working/building/REAL300025241490 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/365 `/scratch/stefan/7787021/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1=CC=CC(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)=C1) `REAL300025241490.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241490 none C#CC1=CC=CC(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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: [35, 35, 35, 35, 35, 35, 16, 6, 16, 4, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 14, 43, 43, 43, 43, 43, 35, 35, 35, 35, 35, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 43, 35] 201 rigid atoms, others: [43, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47]) total number of confs: 153 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: REAL300025241490 none C#CC1=CC=CC(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 201, 201, 201, 201, 127, 82, 127, 65, 82, 43, 43, 43, 43, 43, 40, 23, 40, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 82, 82, 82, 65, 65, 43, 43, 43, 43, 43, 43, 43, 23, 23, 1, 201] 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]) total number of confs: 621 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: REAL300025241490 none C#CC1=CC=CC(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 9, 9, 19, 19, 25, 35, 35, 35, 35, 35, 38, 38, 67, 102, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 19, 19, 19, 25, 25, 35, 35, 35, 35, 35, 35, 35, 67, 67, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 47, 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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 522 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241490 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241490 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241490/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241490 Building REAL300025241491 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241491' /scratch/stefan/7787021/working/building/REAL300025241491 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241491 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241491/0 /scratch/stefan/7787021/working/building/REAL300025241491 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/366 `/scratch/stefan/7787021/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(O)CCCCC1) `REAL300025241491.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241491 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(O)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [153, 143, 94, 94, 94, 94, 94, 71, 30, 71, 13, 1, 1, 1, 1, 1, 1, 1, 153, 201, 201, 201, 201, 201, 201, 201, 201, 153, 153, 153, 143, 143, 94, 94, 94, 94, 94, 94, 94, 30, 30, 1, 603, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 603 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 1344 number of broken/clashed sets: 541 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241491 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(O)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 3, 5, 10, 16, 16, 16, 16, 16, 26, 26, 70, 112, 201, 201, 201, 201, 201, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 16, 16, 16, 16, 16, 16, 16, 70, 70, 201, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 603 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 26, 52] 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, 42]) total number of confs: 508 number of broken/clashed sets: 541 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241491 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(O)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 33, 94, 94, 94, 94, 94, 9, 16, 16, 16, 16, 16, 16, 16, 16, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 17, 17, 94, 48, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 264 number of broken/clashed sets: 541 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241491 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241491 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241491/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241491 Building REAL300025241492 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241492' /scratch/stefan/7787021/working/building/REAL300025241492 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241492 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241492/0 /scratch/stefan/7787021/working/building/REAL300025241492 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/367 `/scratch/stefan/7787021/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(O)CC1) `REAL300025241492.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241492 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 86, 59, 59, 59, 59, 59, 55, 35, 55, 13, 1, 1, 1, 1, 1, 1, 1, 122, 172, 172, 201, 201, 201, 122, 122, 122, 86, 86, 59, 59, 59, 59, 59, 59, 59, 35, 35, 1, 603, 201, 201, 201, 201] 603 rigid atoms, others: [38, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43]) total number of confs: 1363 number of broken/clashed sets: 164 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241492 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 15, 22, 30, 30, 30, 30, 30, 33, 33, 64, 98, 201, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 15, 15, 15, 22, 22, 30, 30, 30, 30, 30, 30, 30, 64, 64, 201, 6, 1, 1, 1, 1] 603 rigid atoms, others: [40, 41, 42, 43, 18, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 504 number of broken/clashed sets: 164 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241492 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 14, 59, 59, 59, 59, 59, 9, 19, 19, 30, 30, 30, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 59, 90, 30, 30, 30, 30] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 276 number of broken/clashed sets: 164 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241492 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241492 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241492/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241492 Building REAL300025241493 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241493' /scratch/stefan/7787021/working/building/REAL300025241493 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241493 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241493/0 /scratch/stefan/7787021/working/building/REAL300025241493 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/368 `/scratch/stefan/7787021/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CS(N)(=O)=O) `REAL300025241493.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241493 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CS(N)(=O)=O NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 14, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 96, 68, 68, 68, 68, 68, 68, 31, 68, 12, 1, 1, 1, 1, 1, 1, 1, 130, 141, 141, 173, 201, 201, 201, 130, 130, 130, 96, 96, 68, 68, 68, 68, 68, 68, 68, 31, 31, 1, 173, 173, 201, 201] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43]) total number of confs: 886 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: REAL300025241493 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CS(N)(=O)=O NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 14, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 2, 2, 8, 17, 68, 68, 68, 68, 68, 6, 9, 9, 16, 30, 30, 30, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 68, 16, 16, 30, 30] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241493 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241493 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241493/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241493 Building REAL300025241494 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241494' /scratch/stefan/7787021/working/building/REAL300025241494 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241494 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241494/0 /scratch/stefan/7787021/working/building/REAL300025241494 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/369 `/scratch/stefan/7787021/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)C=NS1) `REAL300025241494.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241494 none CC1=C(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)C=NS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', '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, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 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: [28, 28, 15, 7, 15, 5, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 21, 72, 72, 72, 72, 72, 28, 28, 28, 28, 28, 28, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 72, 28] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 40, 39] 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, 41, 42, 43, 44]) total number of confs: 190 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: REAL300025241494 none CC1=C(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)C=NS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', '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, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 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: [201, 201, 148, 116, 148, 103, 116, 72, 72, 72, 72, 72, 56, 28, 56, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 116, 116, 116, 103, 103, 72, 72, 72, 72, 72, 72, 72, 28, 28, 1, 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]) total number of confs: 656 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: REAL300025241494 none CC1=C(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)C=NS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', '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, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 12, 12, 18, 28, 28, 28, 28, 28, 34, 34, 66, 105, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 12, 12, 12, 18, 18, 28, 28, 28, 28, 28, 28, 28, 66, 66, 201, 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: 519 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241494 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241494 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241494/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241494 Building REAL300025241495 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241495' /scratch/stefan/7787021/working/building/REAL300025241495 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241495 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241495/0 /scratch/stefan/7787021/working/building/REAL300025241495 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/370 `/scratch/stefan/7787021/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CC(=O)[N-]O1) `REAL300025241495.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241495 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 4, 2, 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, 2, 2, 1, 4] 4 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41]) 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: REAL300025241495 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 1] 4 rigid atoms, others: [41, 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: 17 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: REAL300025241495 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 3] 4 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41]) total number of confs: 24 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241495 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241495 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241495/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241495 Building REAL300025241496 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241496' /scratch/stefan/7787021/working/building/REAL300025241496 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241496 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241496/0 /scratch/stefan/7787021/working/building/REAL300025241496 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/371 `/scratch/stefan/7787021/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)COC1) `REAL300025241496.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241496 none CCC1(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)COC1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 12, 4, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 41, 124, 124, 124, 124, 124, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 23, 23, 124, 12, 12, 12, 12] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 259 number of broken/clashed sets: 192 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241496 none CCC1(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)COC1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 201, 169, 186, 124, 124, 124, 124, 124, 92, 32, 92, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 186, 186, 186, 169, 169, 124, 124, 124, 124, 124, 124, 124, 32, 32, 1, 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]) total number of confs: 688 number of broken/clashed sets: 192 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241496 none CCC1(C(=O)N(C)CC2CCCN2C(=O)CSC2=NNC(=O)[N-]2)COC1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 4, 4, 8, 12, 12, 12, 12, 12, 24, 24, 72, 118, 201, 201, 201, 201, 201, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 8, 8, 12, 12, 12, 12, 12, 12, 12, 72, 72, 201, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 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, 44, 45]) total number of confs: 504 number of broken/clashed sets: 192 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241496 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241496 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241496/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241496 Building REAL300025241497 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241497' /scratch/stefan/7787021/working/building/REAL300025241497 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241497 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241497/0 /scratch/stefan/7787021/working/building/REAL300025241497 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/372 `/scratch/stefan/7787021/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(C)CCCO1) `REAL300025241497.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241497 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(C)CCCO1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [141, 115, 81, 81, 81, 81, 81, 57, 27, 57, 12, 1, 1, 1, 1, 1, 1, 1, 141, 177, 177, 201, 201, 201, 201, 201, 141, 141, 141, 115, 115, 81, 81, 81, 81, 81, 81, 81, 27, 27, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 725 number of broken/clashed sets: 137 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241497 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(C)CCCO1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 8, 13, 20, 20, 20, 20, 20, 28, 28, 64, 103, 201, 201, 201, 201, 201, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 13, 13, 20, 20, 20, 20, 20, 20, 20, 64, 64, 201, 2, 2, 2, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 504 number of broken/clashed sets: 137 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241497 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(C)CCCO1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 29, 81, 81, 81, 81, 81, 10, 15, 15, 20, 20, 20, 20, 20, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 16, 16, 81, 20, 20, 20, 20, 20, 20, 20, 20, 20] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 215 number of broken/clashed sets: 137 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241497 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241497 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241497/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241497 Building REAL300025241498 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241498' /scratch/stefan/7787021/working/building/REAL300025241498 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241498 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241498/0 /scratch/stefan/7787021/working/building/REAL300025241498 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/373 `/scratch/stefan/7787021/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CC(=O)N1) `REAL300025241498.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241498 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 83, 49, 49, 49, 49, 49, 49, 30, 49, 13, 1, 1, 1, 1, 1, 1, 1, 134, 186, 186, 201, 201, 201, 201, 134, 134, 134, 83, 83, 49, 49, 49, 49, 49, 49, 49, 30, 30, 1, 201, 201, 201, 201] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43]) total number of confs: 776 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: REAL300025241498 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 18, 26, 32, 32, 32, 32, 32, 33, 33, 59, 97, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 18, 18, 18, 26, 26, 32, 32, 32, 32, 32, 32, 32, 59, 59, 201, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 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: 495 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: REAL300025241498 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 6, 11, 49, 49, 49, 49, 49, 9, 20, 20, 32, 32, 32, 32, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 49, 32, 32, 32, 32] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 171 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241498 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241498 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241498/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241498 Building REAL300025241499 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241499' /scratch/stefan/7787021/working/building/REAL300025241499 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241499 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241499/0 /scratch/stefan/7787021/working/building/REAL300025241499 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/374 `/scratch/stefan/7787021/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=NOC(CO)=C1) `REAL300025241499.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241499 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=NOC(CO)=C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 8, 12, 1, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [116, 86, 52, 52, 52, 52, 52, 51, 30, 51, 13, 1, 1, 1, 1, 1, 1, 1, 116, 188, 188, 201, 201, 201, 201, 201, 201, 116, 116, 116, 86, 86, 52, 52, 52, 52, 52, 52, 52, 30, 30, 1, 201, 201, 603, 201] 603 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 1324 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: REAL300025241499 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=NOC(CO)=C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 8, 12, 1, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 9, 15, 21, 21, 21, 21, 21, 22, 22, 41, 75, 201, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 8, 1, 9, 9, 9, 15, 15, 21, 21, 21, 21, 21, 21, 21, 41, 41, 201, 8, 8, 24, 1] 603 rigid atoms, others: [45, 18, 20, 21, 22, 23, 24, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 473 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: REAL300025241499 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=NOC(CO)=C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 8, 12, 1, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 12, 52, 52, 52, 52, 52, 7, 17, 17, 21, 21, 21, 21, 58, 21, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 52, 58, 58, 174, 21] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 463 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241499 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241499 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241499/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241499 Building REAL300025241500 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241500' /scratch/stefan/7787021/working/building/REAL300025241500 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241500 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241500/0 /scratch/stefan/7787021/working/building/REAL300025241500 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/375 `/scratch/stefan/7787021/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(C)(C)C) `REAL300025241500.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241500 none CC(=CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 127, 156, 89, 127, 59, 59, 59, 59, 59, 57, 30, 57, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 127, 127, 127, 89, 89, 59, 59, 59, 59, 59, 59, 59, 30, 30, 1, 201, 201, 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]) total number of confs: 792 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: REAL300025241500 none CC(=CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 7, 13, 4, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 59, 59, 59, 59, 59, 30, 31, 31, 31, 30, 30, 30, 30, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 59, 31, 31, 31, 31, 31, 31, 31, 31, 31] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241500 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241500 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241500/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241500 Building REAL300025241501 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241501' /scratch/stefan/7787021/working/building/REAL300025241501 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241501 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241501/0 /scratch/stefan/7787021/working/building/REAL300025241501 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/376 `/scratch/stefan/7787021/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CCCOCC1) `REAL300025241501.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241501 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CCCOCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 94, 70, 70, 70, 70, 70, 58, 29, 58, 13, 1, 1, 1, 1, 1, 1, 1, 114, 187, 187, 201, 201, 201, 201, 201, 201, 114, 114, 114, 94, 94, 70, 70, 70, 70, 70, 70, 70, 29, 29, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 658 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: REAL300025241501 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CCCOCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 15, 22, 22, 22, 22, 22, 27, 27, 61, 101, 201, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 15, 15, 22, 22, 22, 22, 22, 22, 22, 61, 61, 201, 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: 505 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: REAL300025241501 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CCCOCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 25, 70, 70, 70, 70, 70, 10, 20, 20, 22, 22, 22, 22, 22, 22, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 13, 13, 70, 22, 22, 22, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241501 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241501 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241501/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241501 Building REAL300025241502 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241502' /scratch/stefan/7787021/working/building/REAL300025241502 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241502 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241502/0 /scratch/stefan/7787021/working/building/REAL300025241502 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/377 `/scratch/stefan/7787021/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OCC[C@@H]1C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241502.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241502 none C[C@@H]1OCC[C@@H]1C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 7, 12, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 19, 21, 12, 19, 5, 12, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 30, 105, 105, 105, 105, 105, 21, 21, 21, 21, 21, 21, 21, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 19, 19, 105] 201 rigid atoms, others: [45, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49]) total number of confs: 248 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: REAL300025241502 none C[C@@H]1OCC[C@@H]1C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 7, 12, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 197, 201, 150, 197, 105, 105, 105, 105, 105, 87, 33, 87, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 197, 197, 197, 150, 150, 105, 105, 105, 105, 105, 105, 105, 33, 33, 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: 734 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: REAL300025241502 none C[C@@H]1OCC[C@@H]1C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 7, 12, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 1, 3, 3, 7, 7, 11, 21, 21, 21, 21, 21, 30, 30, 73, 111, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 7, 7, 7, 11, 11, 21, 21, 21, 21, 21, 21, 21, 73, 73, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 33, 31] set([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: 513 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241502 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241502 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241502/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241502 Building REAL300025241503 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241503' /scratch/stefan/7787021/working/building/REAL300025241503 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241503 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241503/0 /scratch/stefan/7787021/working/building/REAL300025241503 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/378 `/scratch/stefan/7787021/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CC(F)C1) `REAL300025241503.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241503 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CC(F)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 83, 50, 50, 50, 50, 50, 50, 30, 50, 13, 1, 1, 1, 1, 1, 1, 1, 125, 173, 173, 201, 201, 201, 201, 125, 125, 125, 83, 83, 50, 50, 50, 50, 50, 50, 50, 30, 30, 1, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 756 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: REAL300025241503 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CC(F)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 18, 25, 34, 34, 34, 34, 34, 34, 34, 61, 96, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 18, 18, 18, 25, 25, 34, 34, 34, 34, 34, 34, 34, 61, 61, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 45, 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: 497 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: REAL300025241503 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CC(F)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 2, 2, 6, 11, 50, 50, 50, 50, 50, 9, 21, 21, 34, 34, 34, 34, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 34, 34, 34, 34, 34, 34] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 180 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241503 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241503 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241503/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241503 Building REAL300025241504 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241504' /scratch/stefan/7787021/working/building/REAL300025241504 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241504 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241504/0 /scratch/stefan/7787021/working/building/REAL300025241504 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/379 `/scratch/stefan/7787021/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(O)C(C)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241504.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241504 none CCC(O)C(C)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 7, 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, 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, 194, 201, 173, 194, 127, 173, 107, 127, 70, 70, 70, 70, 70, 59, 31, 59, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 603, 194, 194, 194, 194, 127, 127, 127, 107, 107, 70, 70, 70, 70, 70, 70, 70, 31, 31, 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: 1415 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: REAL300025241504 none CCC(O)C(C)C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 7, 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, 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: [42, 38, 26, 38, 17, 26, 8, 17, 4, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 19, 70, 70, 70, 70, 70, 42, 42, 42, 42, 42, 38, 114, 26, 26, 26, 26, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 70] 603 rigid atoms, others: [16, 45, 43, 44, 10, 11, 12, 13, 14, 15, 48, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 49, 50, 51]) total number of confs: 411 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241504 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241504 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241504/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241504 Building REAL300025241505 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241505' /scratch/stefan/7787021/working/building/REAL300025241505 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241505 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241505/0 /scratch/stefan/7787021/working/building/REAL300025241505 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/380 `/scratch/stefan/7787021/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)OCC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241505.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241505 none CCC(C)(C)OCC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 201, 201, 94, 66, 61, 66, 56, 61, 37, 37, 37, 37, 37, 34, 19, 34, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 94, 94, 61, 61, 61, 56, 56, 37, 37, 37, 37, 37, 37, 37, 19, 19, 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: 837 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: REAL300025241505 none CCC(C)(C)OCC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 51, 25, 51, 51, 12, 6, 5, 6, 3, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 12, 37, 37, 37, 37, 37, 63, 63, 63, 63, 63, 51, 51, 51, 51, 51, 51, 12, 12, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 37] 201 rigid atoms, others: [48, 17, 15, 11, 12, 13, 14, 45, 16, 49, 50, 51, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 52, 53, 54]) total number of confs: 335 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241505 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241505 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241505/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241505 Building REAL300025241506 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241506' /scratch/stefan/7787021/working/building/REAL300025241506 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241506 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241506/0 /scratch/stefan/7787021/working/building/REAL300025241506 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/381 `/scratch/stefan/7787021/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CC1CC(=O)N1) `REAL300025241506.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241506 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CC1CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 73, 48, 48, 48, 48, 48, 44, 27, 44, 13, 1, 1, 1, 1, 1, 1, 1, 100, 147, 147, 154, 201, 201, 201, 201, 100, 100, 100, 73, 73, 48, 48, 48, 48, 48, 48, 48, 27, 27, 1, 154, 154, 201, 201, 201, 201] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 783 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: REAL300025241506 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CC1CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 18, 25, 33, 33, 33, 33, 33, 34, 34, 67, 103, 201, 201, 201, 201, 201, 5, 12, 1, 1, 1, 1, 1, 1, 18, 18, 18, 25, 25, 33, 33, 33, 33, 33, 33, 33, 67, 67, 201, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 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: 541 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: REAL300025241506 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CC1CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 8, 14, 48, 48, 48, 48, 48, 9, 16, 16, 19, 33, 33, 33, 33, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 48, 19, 19, 33, 33, 33, 33] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241506 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241506 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241506/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241506 Building REAL300025241507 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241507' /scratch/stefan/7787021/working/building/REAL300025241507 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241507 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241507/0 /scratch/stefan/7787021/working/building/REAL300025241507 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/382 `/scratch/stefan/7787021/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C(O)C1CCC1) `REAL300025241507.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241507 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C(O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [125, 81, 47, 47, 47, 47, 47, 47, 30, 47, 13, 1, 1, 1, 1, 1, 1, 1, 125, 148, 148, 167, 167, 201, 201, 201, 125, 125, 125, 81, 81, 47, 47, 47, 47, 47, 47, 47, 30, 30, 1, 167, 501, 201, 201, 201, 201, 201, 201, 201] 603 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 1342 number of broken/clashed sets: 169 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241507 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C(O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 25, 29, 41, 41, 41, 41, 41, 41, 41, 73, 114, 201, 201, 201, 201, 201, 6, 14, 1, 6, 1, 1, 1, 1, 25, 25, 25, 29, 29, 41, 41, 41, 41, 41, 41, 41, 73, 73, 201, 6, 18, 1, 1, 1, 1, 1, 1, 1] 603 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 20, 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, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 563 number of broken/clashed sets: 169 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241507 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C(O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 11, 47, 47, 47, 47, 47, 10, 18, 18, 23, 23, 41, 41, 41, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 47, 23, 69, 41, 41, 41, 41, 41, 41, 41] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37, 31] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 284 number of broken/clashed sets: 169 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241507 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241507 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241507/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241507 Building REAL300025241508 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241508' /scratch/stefan/7787021/working/building/REAL300025241508 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241508 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241508/0 /scratch/stefan/7787021/working/building/REAL300025241508 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/383 `/scratch/stefan/7787021/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=NNC(=O)CC1) `REAL300025241508.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241508 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=NNC(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 8, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 81, 52, 52, 52, 52, 52, 49, 29, 49, 13, 1, 1, 1, 1, 1, 1, 1, 102, 155, 155, 201, 201, 201, 201, 201, 201, 102, 102, 102, 81, 81, 52, 52, 52, 52, 52, 52, 52, 29, 29, 1, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 652 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: REAL300025241508 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=NNC(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 8, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 23, 28, 28, 28, 28, 28, 30, 30, 57, 95, 201, 201, 201, 201, 201, 1, 7, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 23, 23, 28, 28, 28, 28, 28, 28, 28, 57, 57, 201, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 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: 499 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: REAL300025241508 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=NNC(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 8, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 14, 52, 52, 52, 52, 52, 10, 17, 17, 28, 28, 28, 28, 28, 28, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 52, 28, 28, 28, 28, 28] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 152 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241508 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241508 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241508/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241508 Building REAL300025241509 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241509' /scratch/stefan/7787021/working/building/REAL300025241509 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241509 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241509/0 /scratch/stefan/7787021/working/building/REAL300025241509 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/384 `/scratch/stefan/7787021/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CCCNC(N)=O) `REAL300025241509.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241509 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CCCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [66, 55, 34, 34, 34, 34, 34, 31, 30, 31, 11, 1, 1, 1, 1, 1, 1, 1, 66, 76, 76, 76, 77, 160, 201, 201, 201, 66, 66, 66, 55, 55, 34, 34, 34, 34, 34, 34, 34, 30, 30, 1, 76, 76, 77, 77, 160, 160, 201, 201, 201] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 850 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: REAL300025241509 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)CCCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [5, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 16, 34, 34, 34, 34, 34, 5, 6, 6, 6, 7, 15, 21, 21, 21, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 34, 6, 6, 7, 7, 15, 15, 21, 21, 21] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241509 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241509 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241509/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241509 Building REAL300025241510 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241510' /scratch/stefan/7787021/working/building/REAL300025241510 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241510 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241510/0 /scratch/stefan/7787021/working/building/REAL300025241510 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/385 `/scratch/stefan/7787021/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CC=NO1) `REAL300025241510.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241510 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CC=NO1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 109, 69, 69, 69, 69, 69, 60, 32, 60, 13, 1, 1, 1, 1, 1, 1, 1, 128, 186, 186, 201, 201, 201, 201, 128, 128, 128, 109, 109, 69, 69, 69, 69, 69, 69, 69, 32, 32, 1, 201, 201] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 745 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: REAL300025241510 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CC=NO1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 9, 15, 23, 30, 30, 30, 30, 30, 34, 34, 65, 105, 201, 201, 201, 201, 201, 1, 9, 1, 1, 1, 1, 1, 15, 15, 15, 23, 23, 30, 30, 30, 30, 30, 30, 30, 65, 65, 201, 1, 1] 201 rigid atoms, others: [40, 41, 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: 525 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: REAL300025241510 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1=CC=NO1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 1, 4, 4, 11, 19, 69, 69, 69, 69, 69, 9, 20, 20, 30, 30, 30, 30, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 69, 30, 30] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 30, 31] set([0, 1, 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]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241510 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241510 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241510/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241510 Building REAL300025241511 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241511' /scratch/stefan/7787021/working/building/REAL300025241511 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241511 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241511/0 /scratch/stefan/7787021/working/building/REAL300025241511 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/386 `/scratch/stefan/7787021/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C12CCC(C1)OC2) `REAL300025241511.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241511 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C12CCC(C1)OC2 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [177, 168, 121, 121, 121, 121, 121, 86, 31, 86, 13, 1, 1, 1, 1, 1, 1, 1, 177, 177, 177, 201, 201, 201, 201, 201, 201, 177, 177, 177, 168, 168, 121, 121, 121, 121, 121, 121, 121, 31, 31, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 651 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: REAL300025241511 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C12CCC(C1)OC2 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 9, 13, 13, 13, 13, 13, 22, 22, 66, 109, 201, 201, 201, 201, 201, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 13, 13, 13, 13, 13, 13, 13, 66, 66, 201, 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: 482 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: REAL300025241511 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C12CCC(C1)OC2 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 26, 50, 121, 121, 121, 121, 121, 9, 10, 10, 13, 13, 13, 13, 13, 13, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 26, 26, 121, 13, 13, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 267 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241511 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241511 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241511/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241511 Building REAL300025241512 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241512' /scratch/stefan/7787021/working/building/REAL300025241512 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241512 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241512/0 /scratch/stefan/7787021/working/building/REAL300025241512 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/387 `/scratch/stefan/7787021/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CC12CC(O)C2) `REAL300025241512.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241512 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CC12CC(O)C2 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [125, 80, 52, 52, 52, 52, 52, 41, 26, 41, 13, 1, 1, 1, 1, 1, 1, 1, 125, 165, 165, 201, 201, 201, 201, 201, 201, 125, 125, 125, 80, 80, 52, 52, 52, 52, 52, 52, 52, 26, 26, 1, 201, 201, 201, 201, 201, 201, 603, 201, 201] 603 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 1326 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: REAL300025241512 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CC12CC(O)C2 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 15, 24, 28, 28, 28, 28, 28, 30, 30, 58, 100, 201, 201, 201, 201, 201, 1, 7, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 24, 24, 28, 28, 28, 28, 28, 28, 28, 58, 58, 201, 1, 1, 1, 1, 1, 1, 6, 1, 1] 603 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 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, 48]) total number of confs: 529 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: REAL300025241512 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1CC12CC(O)C2 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 17, 52, 52, 52, 52, 52, 9, 16, 16, 28, 28, 28, 28, 28, 28, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 52, 28, 28, 28, 28, 28, 28, 84, 28, 28] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 267 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241512 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241512 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241512/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241512 Building REAL300025241513 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241513' /scratch/stefan/7787021/working/building/REAL300025241513 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241513 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241513/0 /scratch/stefan/7787021/working/building/REAL300025241513 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/388 `/scratch/stefan/7787021/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C=CC1=NNC=C1) `REAL300025241513.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241513 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C=CC1=NNC=C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 63, 40, 40, 40, 40, 40, 40, 26, 40, 12, 1, 1, 1, 1, 1, 1, 1, 86, 158, 158, 201, 201, 201, 201, 201, 201, 86, 86, 86, 63, 63, 40, 40, 40, 40, 40, 40, 40, 26, 26, 1, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 701 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: REAL300025241513 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C=CC1=NNC=C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 10, 21, 27, 34, 34, 34, 34, 34, 34, 34, 64, 101, 201, 201, 201, 201, 201, 3, 9, 3, 1, 1, 1, 1, 1, 1, 21, 21, 21, 27, 27, 34, 34, 34, 34, 34, 34, 34, 64, 64, 201, 3, 3, 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: 519 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: REAL300025241513 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C=CC1=NNC=C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 40, 40, 40, 40, 40, 7, 17, 17, 33, 33, 34, 34, 34, 34, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 40, 33, 33, 34, 34, 34] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 163 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241513 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241513 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241513/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241513 Building REAL300025241514 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241514' /scratch/stefan/7787021/working/building/REAL300025241514 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241514 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241514/0 /scratch/stefan/7787021/working/building/REAL300025241514 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/389 `/scratch/stefan/7787021/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(F)F) `REAL300025241514.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241514 none CC(CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(F)F 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens need 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, 154, 132, 154, 99, 132, 60, 60, 60, 60, 60, 54, 30, 54, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 187, 187, 132, 132, 132, 99, 99, 60, 60, 60, 60, 60, 60, 60, 30, 30, 1, 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]) total number of confs: 860 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: REAL300025241514 none CC(CC(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(F)F 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens 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, 27, 13, 8, 13, 4, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 15, 60, 60, 60, 60, 60, 32, 35, 35, 32, 32, 32, 32, 27, 27, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 60, 35] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 40, 43, 41, 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, 44, 45, 46, 47]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241514 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241514 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241514/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241514 Building REAL300025241515 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241515' /scratch/stefan/7787021/working/building/REAL300025241515 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241515 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241515/0 /scratch/stefan/7787021/working/building/REAL300025241515 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/390 `/scratch/stefan/7787021/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C[C@@H]1CCC[C@H]1O) `REAL300025241515.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241515 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C[C@@H]1CCC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [126, 86, 53, 53, 53, 53, 53, 53, 29, 53, 13, 1, 1, 1, 1, 1, 1, 1, 126, 188, 188, 200, 201, 201, 201, 201, 201, 201, 201, 126, 126, 126, 86, 86, 53, 53, 53, 53, 53, 53, 53, 29, 29, 1, 200, 200, 201, 201, 201, 201, 201, 201, 603] 603 rigid atoms, others: [43, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 1382 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: REAL300025241515 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C[C@@H]1CCC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 18, 25, 32, 32, 32, 32, 32, 32, 32, 63, 101, 201, 201, 201, 201, 201, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 25, 25, 32, 32, 32, 32, 32, 32, 32, 63, 63, 201, 5, 5, 1, 1, 1, 1, 1, 1, 6] 603 rigid atoms, others: [46, 47, 48, 49, 50, 51, 20, 21, 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, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52]) total number of confs: 528 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: REAL300025241515 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C[C@@H]1CCC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 11, 53, 53, 53, 53, 53, 9, 19, 19, 26, 32, 32, 32, 32, 32, 32, 32, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 53, 26, 26, 32, 32, 32, 32, 32, 32, 96] 603 rigid atoms, others: [2, 3, 4, 5, 6, 7, 40, 39, 34, 8, 35, 36, 38, 37] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 287 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241515 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241515 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241515/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241515 Building REAL300025241516 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241516' /scratch/stefan/7787021/working/building/REAL300025241516 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241516 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241516/0 /scratch/stefan/7787021/working/building/REAL300025241516 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/391 `/scratch/stefan/7787021/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC=CC[C@H]1C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241516.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241516 none C[C@@H]1CC=CC[C@H]1C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 23, 23, 23, 23, 23, 23, 16, 23, 8, 16, 4, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 30, 96, 96, 96, 96, 96, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 17, 17, 96] 201 rigid atoms, others: [48, 45, 49, 43, 44, 13, 14, 15, 16, 17, 18, 19, 46, 47] 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, 42, 50, 51, 52]) total number of confs: 241 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: REAL300025241516 none C[C@@H]1CC=CC[C@H]1C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 201, 201, 201, 201, 201, 201, 201, 171, 201, 141, 171, 96, 96, 96, 96, 96, 76, 32, 76, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 171, 171, 171, 141, 141, 96, 96, 96, 96, 96, 96, 96, 32, 32, 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: 747 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: REAL300025241516 none C[C@@H]1CC=CC[C@H]1C(=O)N(C)CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 1, 3, 3, 8, 8, 16, 23, 23, 23, 23, 23, 31, 31, 71, 119, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 16, 16, 23, 23, 23, 23, 23, 23, 23, 71, 71, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 7, 8, 9, 34, 35, 32, 36, 37, 5] set([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: 523 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241516 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241516 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241516/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241516 Building REAL300025241517 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241517' /scratch/stefan/7787021/working/building/REAL300025241517 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241517 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241517/0 /scratch/stefan/7787021/working/building/REAL300025241517 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/392 `/scratch/stefan/7787021/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(NC(N)=O)CC1) `REAL300025241517.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241517 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(NC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 122, 95, 95, 95, 95, 95, 86, 31, 86, 13, 1, 1, 1, 1, 1, 1, 1, 168, 176, 176, 201, 201, 201, 201, 201, 201, 168, 168, 168, 122, 122, 95, 95, 95, 95, 95, 95, 95, 31, 31, 1, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 715 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: REAL300025241517 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(NC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 11, 15, 18, 18, 18, 18, 18, 21, 21, 56, 101, 201, 201, 201, 201, 201, 1, 7, 1, 1, 3, 3, 3, 1, 1, 11, 11, 11, 15, 15, 18, 18, 18, 18, 18, 18, 18, 56, 56, 201, 3, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [45, 46, 47, 48, 18, 20, 21, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 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: 470 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: REAL300025241517 none CN(CC1CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(=O)C1(NC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 4, 15, 29, 95, 95, 95, 95, 95, 9, 14, 14, 18, 18, 18, 18, 18, 18, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 95, 18, 18, 18, 18, 18, 18, 18] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 213 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241517 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241517 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241517/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241517 Building REAL300025241518 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241518' /scratch/stefan/7787021/working/building/REAL300025241518 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241518 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241518/0 /scratch/stefan/7787021/working/building/REAL300025241518 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/393 `/scratch/stefan/7787021/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241518.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241518 none CCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 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, 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: [201, 130, 130, 130, 125, 123, 94, 88, 94, 64, 88, 29, 63, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 130, 125, 125, 123, 123, 94, 94, 94, 94, 88, 88, 88, 29, 29, 1] 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]) total number of confs: 956 number of broken/clashed sets: 139 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241518 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241518 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241518/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241518 Building REAL300025241519 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241519' /scratch/stefan/7787021/working/building/REAL300025241519 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241519 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241519/0 /scratch/stefan/7787021/working/building/REAL300025241519 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/394 `/scratch/stefan/7787021/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241519.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241519 none COCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 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, 7, 7] 0 hydrogens need 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, 124, 124, 124, 119, 104, 84, 79, 84, 60, 79, 27, 59, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 197, 197, 124, 119, 119, 104, 104, 84, 84, 84, 84, 79, 79, 79, 27, 27, 1] 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]) total number of confs: 875 number of broken/clashed sets: 151 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241519 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241519 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241519/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241519 Building REAL300025241520 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241520' /scratch/stefan/7787021/working/building/REAL300025241520 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241520 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241520/0 /scratch/stefan/7787021/working/building/REAL300025241520 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/395 `/scratch/stefan/7787021/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241520.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241520 none CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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: [201, 201, 201, 198, 171, 146, 132, 146, 88, 132, 30, 87, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 198, 198, 171, 171, 146, 146, 146, 146, 132, 132, 132, 30, 30, 1] 201 rigid atoms, others: [37, 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]) total number of confs: 804 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241520 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241520 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241520/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241520 Building REAL300025241521 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241521' /scratch/stefan/7787021/working/building/REAL300025241521 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241521 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241521/0 /scratch/stefan/7787021/working/building/REAL300025241521 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/396 `/scratch/stefan/7787021/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241521.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241521 none CC(CCNC(=O)C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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] 0 hydrogens 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, 69, 80, 102, 102, 115, 115, 115, 201, 201, 50, 69, 25, 49, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 102, 102, 102, 102, 115, 201, 201, 201, 201, 201, 69, 69, 69, 25, 25, 1] 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]) total number of confs: 792 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: REAL300025241521 none CC(CCNC(=O)C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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] 0 hydrogens 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, 19, 9, 9, 1, 9, 1, 1, 1, 27, 32, 32, 39, 39, 78, 111, 201, 201, 201, 201, 201, 27, 27, 27, 27, 19, 19, 19, 19, 9, 1, 1, 1, 1, 1, 32, 32, 32, 78, 78, 201] 201 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 31] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41]) total number of confs: 556 number of broken/clashed sets: 126 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241521 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241521 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241521/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241521 Building REAL300025241522 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241522' /scratch/stefan/7787021/working/building/REAL300025241522 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241522 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241522/0 /scratch/stefan/7787021/working/building/REAL300025241522 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/397 `/scratch/stefan/7787021/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241522.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241522 none CC(CCNC(=O)C1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 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, 7, 7] 0 hydrogens 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, 74, 78, 83, 88, 88, 88, 88, 201, 201, 201, 57, 74, 27, 56, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 83, 83, 88, 88, 88, 201, 201, 201, 201, 201, 201, 201, 74, 74, 74, 27, 27, 1] 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]) total number of confs: 678 number of broken/clashed sets: 107 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241522 none CC(CCNC(=O)C1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 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, 7, 7] 0 hydrogens 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, 19, 16, 10, 10, 1, 10, 1, 1, 1, 1, 25, 27, 27, 35, 35, 72, 110, 201, 201, 201, 201, 201, 25, 25, 25, 25, 19, 19, 16, 16, 10, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 72, 72, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 37] set([0, 1, 2, 3, 4, 6, 11, 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]) total number of confs: 537 number of broken/clashed sets: 107 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241522 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241522 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241522/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241522 Building REAL300025241523 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241523' /scratch/stefan/7787021/working/building/REAL300025241523 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241523 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241523/0 /scratch/stefan/7787021/working/building/REAL300025241523 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/398 `/scratch/stefan/7787021/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241523.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241523 none CC(CCNC(=O)C1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 91, 102, 110, 114, 114, 114, 114, 201, 201, 201, 201, 70, 91, 27, 69, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 102, 102, 110, 110, 114, 114, 114, 201, 201, 201, 201, 201, 201, 201, 201, 201, 91, 91, 91, 27, 27, 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: 688 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: REAL300025241523 none CC(CCNC(=O)C1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 16, 8, 8, 1, 8, 1, 1, 1, 1, 1, 23, 26, 26, 32, 32, 68, 111, 201, 201, 201, 201, 201, 23, 23, 23, 23, 19, 19, 16, 16, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 68, 68, 201] 201 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 528 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241523 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241523 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241523/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241523 Building REAL300025241524 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241524' /scratch/stefan/7787021/working/building/REAL300025241524 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241524 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241524/0 /scratch/stefan/7787021/working/building/REAL300025241524 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/399 `/scratch/stefan/7787021/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241524.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241524 none CC(CCNC(=O)C1CCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 84, 92, 96, 101, 101, 101, 101, 201, 201, 201, 201, 201, 65, 84, 27, 65, 12, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 96, 96, 101, 101, 101, 201, 201, 201, 201, 201, 201, 201, 201, 201, 84, 84, 84, 27, 27, 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: 687 number of broken/clashed sets: 97 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241524 none CC(CCNC(=O)C1CCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 25, 25, 30, 30, 63, 105, 201, 201, 201, 201, 201, 22, 22, 22, 22, 17, 17, 15, 15, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 63, 63, 201] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 511 number of broken/clashed sets: 97 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241524 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241524 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241524/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241524 Building REAL300025241525 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241525' /scratch/stefan/7787021/working/building/REAL300025241525 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241525 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241525/0 /scratch/stefan/7787021/working/building/REAL300025241525 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/400 `/scratch/stefan/7787021/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241525.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241525 none CC(CCNC(=O)CC1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 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, 7, 7] 0 hydrogens 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, 84, 90, 90, 90, 90, 167, 201, 201, 59, 77, 29, 58, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 84, 84, 90, 90, 90, 167, 167, 201, 201, 201, 201, 201, 77, 77, 77, 29, 29, 1] 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]) total number of confs: 844 number of broken/clashed sets: 140 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241525 none CC(CCNC(=O)CC1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 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, 7, 7] 0 hydrogens 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, 29, 24, 20, 20, 3, 20, 1, 1, 1, 1, 34, 34, 34, 37, 37, 77, 124, 201, 201, 201, 201, 201, 34, 34, 34, 34, 29, 29, 24, 24, 20, 3, 3, 1, 1, 1, 1, 1, 34, 34, 34, 77, 77, 201] 201 rigid atoms, others: [34, 35, 36, 37, 38, 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, 33, 39, 40, 41, 42, 43, 44]) total number of confs: 560 number of broken/clashed sets: 140 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241525 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241525 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241525/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241525 Building REAL300025241526 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241526' /scratch/stefan/7787021/working/building/REAL300025241526 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241526 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241526/0 /scratch/stefan/7787021/working/building/REAL300025241526 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/401 `/scratch/stefan/7787021/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C(C)(C)F)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241526.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241526 none CC(CCNC(=O)C(C)(C)F)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 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, 7] 0 hydrogens 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, 104, 135, 169, 171, 195, 195, 195, 201, 201, 201, 68, 104, 29, 67, 13, 1, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 169, 169, 171, 171, 195, 201, 201, 201, 201, 201, 201, 104, 104, 104, 29, 29, 1] 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]) total number of confs: 849 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241526 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241526 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241526/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241526 Building REAL300025241527 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241527' /scratch/stefan/7787021/working/building/REAL300025241527 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241527 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241527/0 /scratch/stefan/7787021/working/building/REAL300025241527 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/402 `/scratch/stefan/7787021/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C(C)(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241527.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241527 none CC(CCNC(=O)C(C)(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 5, 5, 15, 15, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 85, 102, 125, 128, 144, 144, 144, 201, 201, 201, 59, 85, 29, 58, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 102, 102, 125, 125, 128, 128, 144, 201, 201, 201, 85, 85, 85, 29, 29, 1] 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]) total number of confs: 941 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241527 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241527 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241527/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241527 Building REAL300025241528 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241528' /scratch/stefan/7787021/working/building/REAL300025241528 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241528 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241528/0 /scratch/stefan/7787021/working/building/REAL300025241528 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/403 `/scratch/stefan/7787021/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241528.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241528 none COCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 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, 3, 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: [201, 200, 155, 155, 155, 145, 128, 100, 84, 100, 60, 84, 27, 59, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 155, 145, 145, 128, 128, 100, 100, 100, 100, 84, 84, 84, 27, 27, 1] 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]) total number of confs: 944 number of broken/clashed sets: 121 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241528 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241528 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241528/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241528 Building REAL300025241529 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241529' /scratch/stefan/7787021/working/building/REAL300025241529 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241529 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241529/0 /scratch/stefan/7787021/working/building/REAL300025241529 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/404 `/scratch/stefan/7787021/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=CC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241529.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241529 none CC(CCNC(=O)C1=CC=CC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 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: [115, 103, 115, 156, 180, 201, 201, 201, 201, 201, 201, 201, 201, 65, 103, 26, 65, 13, 1, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 156, 156, 180, 180, 201, 201, 201, 201, 201, 103, 103, 103, 26, 26, 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: 856 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: REAL300025241529 none CC(CCNC(=O)C1=CC=CC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 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, 8, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 23, 23, 34, 34, 66, 102, 201, 201, 201, 201, 201, 17, 17, 17, 17, 10, 10, 7, 7, 1, 1, 1, 1, 1, 23, 23, 23, 66, 66, 201] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 35, 36, 37] set([0, 1, 2, 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]) total number of confs: 528 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241529 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241529 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241529/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241529 Building REAL300025241530 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241530' /scratch/stefan/7787021/working/building/REAL300025241530 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241530 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241530/0 /scratch/stefan/7787021/working/building/REAL300025241530 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/405 `/scratch/stefan/7787021/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=NC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241530.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241530 none CC(CCNC(=O)C1=CC=NC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 130, 152, 180, 190, 201, 201, 201, 201, 201, 201, 201, 201, 97, 130, 32, 96, 13, 1, 1, 1, 1, 1, 1, 1, 152, 152, 152, 152, 180, 180, 190, 190, 201, 201, 201, 201, 201, 130, 130, 130, 32, 32, 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: 783 number of broken/clashed sets: 106 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241530 none CC(CCNC(=O)C1=CC=NC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 13, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 20, 30, 30, 38, 38, 74, 121, 201, 201, 201, 201, 201, 20, 20, 20, 20, 15, 15, 11, 11, 3, 1, 1, 1, 1, 30, 30, 30, 74, 74, 201] 201 rigid atoms, others: [34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43]) total number of confs: 551 number of broken/clashed sets: 106 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241530 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241530 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241530/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241530 Building REAL300025241531 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241531' /scratch/stefan/7787021/working/building/REAL300025241531 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241531 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241531/0 /scratch/stefan/7787021/working/building/REAL300025241531 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/406 `/scratch/stefan/7787021/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=C(F)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241531.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241531 none CC(CCNC(=O)C1=CC=C(F)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [148, 124, 148, 176, 189, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 124, 31, 89, 13, 1, 1, 1, 1, 1, 1, 1, 148, 148, 148, 148, 176, 176, 189, 189, 201, 201, 201, 201, 201, 124, 124, 124, 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: 796 number of broken/clashed sets: 108 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241531 none CC(CCNC(=O)C1=CC=C(F)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [21, 13, 12, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 21, 31, 31, 38, 38, 72, 121, 201, 201, 201, 201, 201, 21, 21, 21, 21, 15, 15, 12, 12, 3, 1, 1, 1, 1, 31, 31, 31, 72, 72, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44]) total number of confs: 539 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241531 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241531 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241531/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241531 Building REAL300025241532 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241532' /scratch/stefan/7787021/working/building/REAL300025241532 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241532 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241532/0 /scratch/stefan/7787021/working/building/REAL300025241532 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/407 `/scratch/stefan/7787021/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241532.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241532 none CCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 122, 122, 122, 122, 109, 101, 100, 101, 74, 100, 30, 73, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 122, 122, 122, 109, 109, 101, 101, 101, 101, 100, 100, 100, 30, 30, 1] 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]) total number of confs: 870 number of broken/clashed sets: 140 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241532 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241532 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241532/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241532 Building REAL300025241533 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241533' /scratch/stefan/7787021/working/building/REAL300025241533 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241533 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241533/0 /scratch/stefan/7787021/working/building/REAL300025241533 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/408 `/scratch/stefan/7787021/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241533.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241533 none CC(CCNC(=O)C1=CC=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 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: [144, 124, 144, 161, 167, 171, 171, 171, 201, 201, 201, 201, 201, 94, 124, 32, 94, 13, 1, 1, 1, 1, 1, 1, 1, 144, 144, 144, 144, 161, 161, 167, 167, 171, 201, 201, 201, 201, 124, 124, 124, 32, 32, 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: 707 number of broken/clashed sets: 105 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241533 none CC(CCNC(=O)C1=CC=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 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: [21, 15, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 21, 27, 27, 34, 34, 75, 123, 201, 201, 201, 201, 201, 21, 21, 21, 21, 17, 17, 14, 14, 5, 1, 1, 1, 1, 27, 27, 27, 75, 75, 201] 201 rigid atoms, others: [34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43]) total number of confs: 547 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241533 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241533 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241533/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241533 Building REAL300025241534 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241534' /scratch/stefan/7787021/working/building/REAL300025241534 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241534 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241534/0 /scratch/stefan/7787021/working/building/REAL300025241534 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/409 `/scratch/stefan/7787021/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1=CC=CS1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241534.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241534 none CC(CCNC(=O)CC1=CC=CS1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 1, 1, 1, 1, 14, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [67, 59, 67, 67, 71, 71, 71, 71, 165, 201, 201, 201, 201, 45, 59, 24, 44, 12, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 67, 71, 71, 71, 165, 165, 201, 201, 201, 59, 59, 59, 24, 24, 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: 764 number of broken/clashed sets: 130 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241534 none CC(CCNC(=O)CC1=CC=CS1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 1, 1, 1, 1, 14, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [25, 23, 20, 14, 14, 3, 14, 1, 1, 1, 1, 1, 1, 25, 27, 27, 29, 29, 59, 97, 201, 201, 201, 201, 201, 25, 25, 25, 25, 23, 23, 20, 20, 14, 3, 3, 1, 1, 1, 27, 27, 27, 59, 59, 201] 201 rigid atoms, others: [36, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 504 number of broken/clashed sets: 130 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241534 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241534 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241534/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241534 Building REAL300025241535 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241535' /scratch/stefan/7787021/working/building/REAL300025241535 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241535 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241535/0 /scratch/stefan/7787021/working/building/REAL300025241535 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/410 `/scratch/stefan/7787021/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=CO1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241535.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241535 none CC(CCNC(=O)C1=CC=CO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 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: [126, 108, 126, 160, 181, 201, 201, 201, 201, 201, 201, 201, 65, 108, 27, 65, 13, 1, 1, 1, 1, 1, 1, 1, 126, 126, 126, 126, 160, 160, 181, 181, 201, 201, 201, 201, 108, 108, 108, 27, 27, 1] 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]) total number of confs: 828 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: REAL300025241535 none CC(CCNC(=O)C1=CC=CO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 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: [15, 9, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 23, 23, 36, 36, 66, 104, 201, 201, 201, 201, 201, 15, 15, 15, 15, 9, 9, 6, 6, 1, 1, 1, 1, 23, 23, 23, 66, 66, 201] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35] set([0, 1, 2, 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]) total number of confs: 512 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241535 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241535 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241535/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241535 Building REAL300025241536 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241536' /scratch/stefan/7787021/working/building/REAL300025241536 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241536 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241536/0 /scratch/stefan/7787021/working/building/REAL300025241536 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/411 `/scratch/stefan/7787021/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241536.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241536 none CC(=O)NCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 4, 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, 7] 0 hydrogens need 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, 153, 153, 153, 127, 113, 94, 87, 94, 75, 87, 28, 74, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 193, 193, 153, 127, 127, 113, 113, 94, 94, 94, 94, 87, 87, 87, 28, 28, 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: 873 number of broken/clashed sets: 139 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241536 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241536 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241536/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241536 Building REAL300025241537 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241537' /scratch/stefan/7787021/working/building/REAL300025241537 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241537 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241537/0 /scratch/stefan/7787021/working/building/REAL300025241537 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/412 `/scratch/stefan/7787021/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)SC=C1) `REAL300025241537.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241537 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 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, 7, 7, 7] 0 hydrogens need 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, 119, 119, 119, 118, 107, 89, 77, 89, 56, 77, 25, 55, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 119, 118, 118, 107, 107, 89, 89, 89, 89, 77, 77, 77, 25, 25, 1, 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]) total number of confs: 639 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241537 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 11, 18, 18, 23, 23, 32, 32, 68, 104, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 5, 9, 9, 11, 11, 18, 18, 18, 18, 23, 23, 23, 68, 68, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 43, 44, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 542 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241537 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241537 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241537/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241537 Building REAL300025241538 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241538' /scratch/stefan/7787021/working/building/REAL300025241538 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241538 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241538/0 /scratch/stefan/7787021/working/building/REAL300025241538 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/413 `/scratch/stefan/7787021/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)S1) `REAL300025241538.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241538 none CC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need 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, 194, 194, 181, 157, 117, 100, 117, 67, 100, 25, 67, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 194, 181, 181, 157, 157, 117, 117, 117, 117, 100, 100, 100, 25, 25, 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: 812 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241538 none CC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations 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, 4, 4, 4, 10, 13, 19, 19, 25, 25, 34, 34, 65, 101, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 4, 10, 10, 13, 13, 19, 19, 19, 19, 25, 25, 25, 65, 65, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 508 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241538 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241538 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241538/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241538 Building REAL300025241539 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241539' /scratch/stefan/7787021/working/building/REAL300025241539 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241539 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241539/0 /scratch/stefan/7787021/working/building/REAL300025241539 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/414 `/scratch/stefan/7787021/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C=CC1=CC=CO1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241539.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241539 none CC(CCNC(=O)C=CC1=CC=CO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 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, 89, 98, 127, 159, 180, 180, 180, 201, 201, 201, 201, 201, 201, 78, 89, 29, 78, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 127, 127, 159, 159, 180, 201, 201, 201, 201, 201, 89, 89, 89, 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: 834 number of broken/clashed sets: 135 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241539 none CC(CCNC(=O)C=CC1=CC=CO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 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: [24, 18, 18, 9, 9, 3, 8, 3, 1, 1, 1, 1, 1, 1, 24, 29, 29, 33, 33, 73, 107, 201, 201, 201, 201, 201, 24, 24, 24, 24, 20, 20, 17, 17, 9, 4, 3, 1, 1, 1, 29, 29, 29, 73, 73, 201] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45]) total number of confs: 549 number of broken/clashed sets: 135 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241539 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241539 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241539/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241539 Building REAL300025241540 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241540' /scratch/stefan/7787021/working/building/REAL300025241540 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241540 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241540/0 /scratch/stefan/7787021/working/building/REAL300025241540 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/415 `/scratch/stefan/7787021/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=CC=C1F)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241540.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241540 none CC(CCNC(=O)C1=CC=CC=C1F)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [127, 103, 127, 153, 167, 189, 189, 189, 201, 201, 190, 201, 201, 201, 70, 103, 27, 69, 13, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 153, 153, 167, 167, 189, 201, 201, 201, 201, 103, 103, 103, 27, 27, 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: 839 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241540 none CC(CCNC(=O)C1=CC=CC=C1F)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [22, 15, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 22, 32, 32, 39, 39, 74, 109, 201, 201, 201, 201, 201, 22, 22, 22, 22, 16, 16, 14, 14, 4, 1, 1, 1, 1, 32, 32, 32, 74, 74, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44]) total number of confs: 546 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241540 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241540 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241540/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241540 Building REAL300025241541 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241541' /scratch/stefan/7787021/working/building/REAL300025241541 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241541 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241541/0 /scratch/stefan/7787021/working/building/REAL300025241541 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/416 `/scratch/stefan/7787021/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=CC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241541.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241541 none CC(CCNC(=O)C1=CC=CC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [148, 124, 148, 178, 193, 201, 201, 201, 201, 201, 201, 201, 201, 94, 124, 31, 94, 13, 1, 1, 1, 1, 1, 1, 1, 148, 148, 148, 148, 178, 178, 193, 193, 201, 201, 201, 201, 201, 201, 124, 124, 124, 31, 31, 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: 792 number of broken/clashed sets: 105 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241541 none CC(CCNC(=O)C1=CC=CC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [21, 12, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 21, 29, 29, 38, 38, 75, 121, 201, 201, 201, 201, 201, 21, 21, 21, 21, 14, 14, 10, 10, 3, 1, 1, 1, 1, 1, 29, 29, 29, 75, 75, 201] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44]) total number of confs: 553 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241541 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241541 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241541/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241541 Building REAL300025241542 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241542' /scratch/stefan/7787021/working/building/REAL300025241542 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241542 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241542/0 /scratch/stefan/7787021/working/building/REAL300025241542 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/417 `/scratch/stefan/7787021/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241542.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241542 none CC(C)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 126, 126, 126, 126, 120, 105, 92, 105, 65, 92, 25, 64, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 126, 126, 126, 120, 120, 105, 105, 105, 105, 92, 92, 92, 25, 25, 1] 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]) total number of confs: 918 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241542 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241542 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241542/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241542 Building REAL300025241543 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241543' /scratch/stefan/7787021/working/building/REAL300025241543 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241543 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241543/0 /scratch/stefan/7787021/working/building/REAL300025241543 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/418 `/scratch/stefan/7787021/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241543.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241543 none CC(CCNC(=O)C1CCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 81, 87, 90, 94, 94, 94, 94, 201, 201, 201, 201, 201, 65, 81, 26, 64, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 90, 90, 94, 94, 94, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 81, 81, 81, 26, 26, 1] 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]) total number of confs: 662 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241543 none CC(CCNC(=O)C1CCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 14, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 23, 27, 27, 32, 32, 65, 107, 201, 201, 201, 201, 201, 23, 23, 23, 23, 17, 17, 14, 14, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 65, 65, 201] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 44, 40, 43, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 45, 46, 47, 48, 49, 50]) total number of confs: 525 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241543 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241543 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241543/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241543 Building REAL300025241544 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241544' /scratch/stefan/7787021/working/building/REAL300025241544 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241544 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241544/0 /scratch/stefan/7787021/working/building/REAL300025241544 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/419 `/scratch/stefan/7787021/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CN=CC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241544.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241544 none CC(CCNC(=O)C1=CN=CC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 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: [128, 107, 128, 160, 184, 201, 201, 201, 201, 201, 201, 201, 201, 70, 107, 29, 70, 13, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 128, 160, 160, 184, 184, 201, 201, 201, 201, 107, 107, 107, 29, 29, 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: 830 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: REAL300025241544 none CC(CCNC(=O)C1=CN=CC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 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: [19, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 26, 26, 37, 37, 66, 105, 201, 201, 201, 201, 201, 19, 19, 19, 19, 12, 12, 7, 7, 2, 1, 1, 1, 26, 26, 26, 66, 66, 201] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 35, 36] set([0, 1, 2, 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]) total number of confs: 519 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241544 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241544 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241544/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241544 Building REAL300025241545 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241545' /scratch/stefan/7787021/working/building/REAL300025241545 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241545 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241545/0 /scratch/stefan/7787021/working/building/REAL300025241545 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/420 `/scratch/stefan/7787021/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241545.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241545 none CC1=CC=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 98, 98, 98, 96, 89, 80, 68, 80, 48, 68, 25, 47, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 98, 96, 96, 89, 89, 80, 80, 80, 80, 68, 68, 68, 25, 25, 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: 552 number of broken/clashed sets: 104 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241545 none CC1=CC=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 201 conformations 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, 14, 19, 19, 24, 24, 30, 30, 60, 101, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 8, 13, 13, 15, 15, 19, 19, 19, 19, 24, 24, 24, 60, 60, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 515 number of broken/clashed sets: 104 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241545 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241545 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241545/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241545 Building REAL300025241546 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241546' /scratch/stefan/7787021/working/building/REAL300025241546 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241546 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241546/0 /scratch/stefan/7787021/working/building/REAL300025241546 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/421 `/scratch/stefan/7787021/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241546.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241546 none CC(CCNC(=O)CC1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 80, 86, 86, 86, 86, 193, 201, 201, 201, 201, 63, 71, 27, 62, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 80, 80, 86, 86, 86, 193, 193, 201, 201, 201, 201, 201, 201, 201, 201, 201, 71, 71, 71, 27, 27, 1] 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]) total number of confs: 774 number of broken/clashed sets: 137 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241546 none CC(CCNC(=O)CC1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 23, 20, 20, 5, 20, 1, 1, 1, 1, 1, 1, 30, 30, 30, 32, 32, 71, 114, 201, 201, 201, 201, 201, 30, 30, 30, 30, 27, 27, 23, 23, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 71, 71, 201] 201 rigid atoms, others: [43, 36, 37, 38, 7, 8, 9, 10, 11, 12, 44, 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, 45, 46, 47, 48, 49, 50]) total number of confs: 533 number of broken/clashed sets: 137 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241546 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241546 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241546/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241546 Building REAL300025241547 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241547' /scratch/stefan/7787021/working/building/REAL300025241547 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241547 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241547/0 /scratch/stefan/7787021/working/building/REAL300025241547 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/422 `/scratch/stefan/7787021/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241547.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241547 none CC(CCNC(=O)CCC1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 51, 51, 51, 51, 148, 157, 201, 201, 201, 201, 51, 51, 29, 50, 13, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 51, 51, 51, 148, 148, 167, 167, 201, 201, 201, 201, 201, 201, 201, 201, 201, 51, 51, 51, 29, 29, 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: 856 number of broken/clashed sets: 157 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241547 none CC(CCNC(=O)CCC1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 25, 6, 25, 4, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 65, 106, 201, 201, 201, 201, 201, 28, 28, 28, 28, 28, 28, 25, 25, 25, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 65, 65, 201] 201 rigid atoms, others: [45, 43, 39, 8, 9, 10, 11, 12, 13, 46, 44, 40, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 504 number of broken/clashed sets: 157 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241547 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241547 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241547/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241547 Building REAL300025241548 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241548' /scratch/stefan/7787021/working/building/REAL300025241548 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241548 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241548/0 /scratch/stefan/7787021/working/building/REAL300025241548 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/423 `/scratch/stefan/7787021/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=CC(F)=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241548.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241548 none CC(CCNC(=O)C1=CC=CC(F)=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [71, 62, 71, 72, 73, 73, 73, 73, 201, 201, 201, 201, 201, 201, 51, 62, 25, 50, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 72, 72, 73, 73, 73, 201, 201, 201, 201, 62, 62, 62, 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: 454 number of broken/clashed sets: 79 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241548 none CC(CCNC(=O)C1=CC=CC(F)=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [14, 10, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 14, 20, 20, 24, 24, 48, 85, 201, 201, 201, 201, 201, 14, 14, 14, 14, 11, 11, 11, 11, 5, 1, 1, 1, 1, 20, 20, 20, 48, 48, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44]) total number of confs: 450 number of broken/clashed sets: 79 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241548 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241548 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241548/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241548 Building REAL300025241549 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241549' /scratch/stefan/7787021/working/building/REAL300025241549 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241549 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241549/0 /scratch/stefan/7787021/working/building/REAL300025241549 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/424 `/scratch/stefan/7787021/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=CS1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241549.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241549 none CC(CCNC(=O)C1=CC=CS1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 1, 14, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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] 0 hydrogens 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, 102, 120, 157, 179, 192, 192, 192, 201, 201, 201, 201, 70, 102, 27, 70, 13, 1, 1, 1, 1, 1, 1, 1, 120, 120, 120, 120, 157, 157, 179, 179, 192, 201, 201, 201, 102, 102, 102, 27, 27, 1] 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]) total number of confs: 807 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241549 none CC(CCNC(=O)C1=CC=CS1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 1, 14, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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] 0 hydrogens 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, 11, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 18, 24, 24, 33, 33, 62, 101, 201, 201, 201, 201, 201, 18, 18, 18, 18, 11, 11, 10, 10, 4, 1, 1, 1, 24, 24, 24, 62, 62, 201] 201 rigid atoms, others: [33, 34, 35, 5, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 496 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241549 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241549 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241549/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241549 Building REAL300025241550 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241550' /scratch/stefan/7787021/working/building/REAL300025241550 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241550 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241550/0 /scratch/stefan/7787021/working/building/REAL300025241550 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/425 `/scratch/stefan/7787021/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=N1) `REAL300025241550.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241550 none CC1=CN=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 161, 147, 117, 78, 117, 65, 79, 41, 65, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 161, 161, 147, 147, 117, 117, 117, 117, 79, 79, 79, 41, 41, 1, 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]) total number of confs: 902 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241550 none CC1=CN=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 2, 2, 2, 10, 14, 23, 23, 36, 36, 56, 56, 74, 112, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 2, 10, 10, 16, 16, 23, 23, 23, 23, 36, 36, 36, 74, 74, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 24, 25, 29] set([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: 556 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241550 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241550 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241550/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241550 Building REAL300025241551 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241551' /scratch/stefan/7787021/working/building/REAL300025241551 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241551 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241551/0 /scratch/stefan/7787021/working/building/REAL300025241551 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/426 `/scratch/stefan/7787021/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1=CSC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241551.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241551 none CC(CCNC(=O)CC1=CSC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [53, 50, 53, 53, 53, 55, 55, 55, 122, 201, 201, 201, 201, 40, 50, 20, 39, 13, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 53, 55, 122, 122, 201, 201, 201, 50, 50, 50, 20, 20, 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: 640 number of broken/clashed sets: 83 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241551 none CC(CCNC(=O)CC1=CSC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [16, 16, 16, 9, 9, 2, 9, 1, 1, 1, 1, 1, 1, 16, 18, 18, 24, 24, 59, 96, 201, 201, 201, 201, 201, 16, 16, 16, 16, 16, 16, 16, 16, 9, 2, 2, 1, 1, 1, 18, 18, 18, 59, 59, 201] 201 rigid atoms, others: [36, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 484 number of broken/clashed sets: 83 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241551 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241551 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241551/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241551 Building REAL300025241552 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241552' /scratch/stefan/7787021/working/building/REAL300025241552 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241552 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241552/0 /scratch/stefan/7787021/working/building/REAL300025241552 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/427 `/scratch/stefan/7787021/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CC1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241552.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241552 none CC(CCNC(=O)C1CC1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 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, 7, 7] 0 hydrogens 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, 68, 74, 86, 95, 95, 95, 95, 201, 201, 201, 50, 68, 24, 49, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 86, 86, 95, 95, 95, 201, 201, 201, 201, 201, 201, 201, 68, 68, 68, 24, 24, 1] 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]) total number of confs: 733 number of broken/clashed sets: 119 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241552 none CC(CCNC(=O)C1CC1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 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, 7, 7] 0 hydrogens 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, 19, 17, 11, 11, 1, 11, 1, 1, 1, 1, 25, 27, 27, 33, 33, 68, 104, 201, 201, 201, 201, 201, 25, 25, 25, 25, 20, 20, 17, 17, 11, 1, 1, 1, 1, 2, 2, 2, 27, 27, 27, 68, 68, 201] 201 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 6, 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: 539 number of broken/clashed sets: 119 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241552 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241552 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241552/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241552 Building REAL300025241553 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241553' /scratch/stefan/7787021/working/building/REAL300025241553 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241553 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241553/0 /scratch/stefan/7787021/working/building/REAL300025241553 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/428 `/scratch/stefan/7787021/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1) `REAL300025241553.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241553 none CC1=CC=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 60, 201, 201, 58, 58, 58, 58, 58, 57, 51, 57, 41, 51, 22, 41, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 59, 201, 201, 58, 58, 58, 58, 58, 57, 57, 57, 57, 51, 51, 51, 22, 22, 1, 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]) total number of confs: 637 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241553 none CC1=CC=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 10, 11, 12, 12, 20, 20, 24, 24, 52, 86, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 5, 10, 10, 12, 12, 12, 12, 12, 12, 20, 20, 20, 52, 52, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 47, 25, 29, 30, 31] set([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]) total number of confs: 469 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241553 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241553 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241553/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241553 Building REAL300025241554 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241554' /scratch/stefan/7787021/working/building/REAL300025241554 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241554 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241554/0 /scratch/stefan/7787021/working/building/REAL300025241554 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/429 `/scratch/stefan/7787021/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241554.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241554 none CCOCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 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, 7, 7] 0 hydrogens need 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, 124, 124, 124, 118, 104, 85, 75, 85, 55, 75, 29, 54, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 190, 190, 124, 118, 118, 104, 104, 85, 85, 85, 85, 75, 75, 75, 29, 29, 1] 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]) total number of confs: 943 number of broken/clashed sets: 137 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241554 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241554 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241554/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241554 Building REAL300025241555 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241555' /scratch/stefan/7787021/working/building/REAL300025241555 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241555 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241555/0 /scratch/stefan/7787021/working/building/REAL300025241555 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/430 `/scratch/stefan/7787021/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241555.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241555 none CC(C)=CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 121, 121, 121, 121, 115, 97, 84, 97, 62, 84, 24, 61, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 121, 121, 121, 115, 115, 97, 97, 97, 97, 84, 84, 84, 24, 24, 1] 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]) total number of confs: 777 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241555 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241555 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241555/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241555 Building REAL300025241556 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241556' /scratch/stefan/7787021/working/building/REAL300025241556 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241556 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241556/0 /scratch/stefan/7787021/working/building/REAL300025241556 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/431 `/scratch/stefan/7787021/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=COCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241556.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241556 none CC(CCNC(=O)C1=COCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 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: [130, 111, 130, 167, 188, 201, 201, 201, 201, 201, 201, 201, 201, 74, 111, 26, 73, 13, 1, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 167, 167, 188, 188, 201, 201, 201, 201, 201, 201, 111, 111, 111, 26, 26, 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: 820 number of broken/clashed sets: 83 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241556 none CC(CCNC(=O)C1=COCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 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, 11, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 16, 22, 22, 32, 32, 65, 103, 201, 201, 201, 201, 201, 16, 16, 16, 16, 12, 12, 10, 10, 4, 1, 1, 1, 1, 1, 22, 22, 22, 65, 65, 201] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44]) total number of confs: 510 number of broken/clashed sets: 83 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241556 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241556 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241556/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241556 Building REAL300025241557 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241557' /scratch/stefan/7787021/working/building/REAL300025241557 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241557 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241557/0 /scratch/stefan/7787021/working/building/REAL300025241557 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/432 `/scratch/stefan/7787021/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=[N+]([O-])C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241557.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241557 none CC(CCNC(=O)C1=CC=[N+]([O-])C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 133, 155, 177, 189, 201, 201, 201, 201, 201, 201, 201, 201, 201, 99, 133, 32, 99, 13, 1, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 177, 177, 189, 189, 201, 201, 201, 201, 201, 133, 133, 133, 32, 32, 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: 765 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: REAL300025241557 none CC(CCNC(=O)C1=CC=[N+]([O-])C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 11, 12, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 18, 26, 26, 35, 35, 71, 120, 201, 201, 201, 201, 201, 18, 18, 18, 18, 13, 13, 12, 12, 3, 1, 1, 1, 1, 26, 26, 26, 71, 71, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44]) total number of confs: 529 number of broken/clashed sets: 110 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241557 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241557 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241557/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241557 Building REAL300025241558 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241558' /scratch/stefan/7787021/working/building/REAL300025241558 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241558 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241558/0 /scratch/stefan/7787021/working/building/REAL300025241558 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/433 `/scratch/stefan/7787021/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CC2C=CC1C2)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241558.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241558 none CC(CCNC(=O)C1CC2C=CC1C2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [118, 101, 118, 144, 157, 163, 163, 163, 201, 201, 201, 201, 201, 201, 67, 101, 28, 67, 13, 1, 1, 1, 1, 1, 1, 1, 118, 118, 118, 118, 144, 144, 157, 157, 163, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 101, 101, 28, 28, 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: 804 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241558 none CC(CCNC(=O)C1CC2C=CC1C2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [19, 14, 14, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 19, 23, 23, 31, 31, 62, 99, 201, 201, 201, 201, 201, 19, 19, 19, 19, 15, 15, 14, 14, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 62, 62, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 40, 43, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 498 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241558 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241558 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241558/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241558 Building REAL300025241559 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241559' /scratch/stefan/7787021/working/building/REAL300025241559 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241559 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241559/0 /scratch/stefan/7787021/working/building/REAL300025241559 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/434 `/scratch/stefan/7787021/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241559.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241559 none CC(=O)NC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 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, 6, 4, 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, 7, 7, 7] 0 hydrogens need 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, 151, 199, 151, 151, 148, 126, 102, 94, 102, 66, 94, 28, 65, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 199, 199, 199, 199, 151, 148, 148, 126, 126, 102, 102, 102, 102, 94, 94, 94, 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: 871 number of broken/clashed sets: 118 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241559 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241559 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241559/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241559 Building REAL300025241560 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241560' /scratch/stefan/7787021/working/building/REAL300025241560 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241560 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241560/0 /scratch/stefan/7787021/working/building/REAL300025241560 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/435 `/scratch/stefan/7787021/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=NNC(=O)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241560.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241560 none CC(CCNC(=O)C1=NNC(=O)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 8, 8, 1, 11, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 91, 112, 144, 169, 198, 198, 198, 201, 201, 201, 201, 201, 201, 58, 91, 28, 57, 13, 1, 1, 1, 1, 1, 1, 1, 112, 112, 112, 112, 144, 144, 169, 169, 198, 201, 201, 201, 91, 91, 91, 28, 28, 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: 847 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: REAL300025241560 none CC(CCNC(=O)C1=NNC(=O)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 8, 8, 1, 11, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 16, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 23, 32, 32, 45, 45, 84, 120, 201, 201, 201, 201, 201, 23, 23, 23, 23, 16, 16, 11, 11, 5, 1, 1, 1, 32, 32, 32, 84, 84, 201] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 581 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241560 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241560 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241560/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241560 Building REAL300025241561 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241561' /scratch/stefan/7787021/working/building/REAL300025241561 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241561 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241561/0 /scratch/stefan/7787021/working/building/REAL300025241561 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/436 `/scratch/stefan/7787021/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)O1) `REAL300025241561.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241561 none CC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 182, 157, 118, 100, 118, 67, 100, 28, 66, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 182, 182, 157, 157, 118, 118, 118, 118, 100, 100, 100, 28, 28, 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: 844 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: REAL300025241561 none CC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 1, 7, 9, 18, 18, 25, 25, 37, 37, 66, 101, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 7, 7, 10, 10, 18, 18, 18, 18, 25, 25, 25, 66, 66, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 24, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 519 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241561 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241561 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241561/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241561 Building REAL300025241562 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241562' /scratch/stefan/7787021/working/building/REAL300025241562 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241562 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241562/0 /scratch/stefan/7787021/working/building/REAL300025241562 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/437 `/scratch/stefan/7787021/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1CCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241562.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241562 none CC(CCNC(=O)CC1CCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 62, 65, 65, 65, 65, 177, 201, 201, 201, 201, 201, 51, 59, 25, 51, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 62, 62, 65, 65, 65, 177, 177, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 59, 59, 59, 25, 25, 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: 792 number of broken/clashed sets: 132 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241562 none CC(CCNC(=O)CC1CCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 29, 26, 20, 20, 5, 20, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 33, 33, 67, 101, 201, 201, 201, 201, 201, 30, 30, 30, 30, 29, 29, 26, 26, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 67, 67, 201] 201 rigid atoms, others: [45, 11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 46, 44, 40, 43, 41, 47, 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, 48, 49, 50, 51, 52, 53]) total number of confs: 514 number of broken/clashed sets: 132 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241562 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241562 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241562/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241562 Building REAL300025241563 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241563' /scratch/stefan/7787021/working/building/REAL300025241563 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241563 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241563/0 /scratch/stefan/7787021/working/building/REAL300025241563 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/438 `/scratch/stefan/7787021/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241563.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241563 none CC(CCNC(=O)C1CCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 88, 113, 142, 165, 175, 175, 175, 201, 201, 201, 201, 58, 88, 28, 57, 13, 1, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 142, 142, 165, 165, 175, 201, 201, 201, 201, 201, 201, 201, 88, 88, 88, 28, 28, 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: 867 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241563 none CC(CCNC(=O)C1CCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 23, 32, 32, 41, 41, 78, 116, 201, 201, 201, 201, 201, 23, 23, 23, 23, 18, 18, 12, 12, 5, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 78, 78, 201] 201 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45]) total number of confs: 567 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241563 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241563 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241563/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241563 Building REAL300025241564 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241564' /scratch/stefan/7787021/working/building/REAL300025241564 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241564 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241564/0 /scratch/stefan/7787021/working/building/REAL300025241564 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/439 `/scratch/stefan/7787021/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241564.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241564 none CSCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 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, 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: [201, 201, 124, 124, 124, 118, 102, 78, 74, 78, 54, 74, 26, 53, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 124, 118, 118, 102, 102, 78, 78, 78, 78, 74, 74, 74, 26, 26, 1] 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]) total number of confs: 962 number of broken/clashed sets: 139 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241564 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241564 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241564/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241564 Building REAL300025241565 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241565' /scratch/stefan/7787021/working/building/REAL300025241565 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241565 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241565/0 /scratch/stefan/7787021/working/building/REAL300025241565 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/440 `/scratch/stefan/7787021/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=NO1) `REAL300025241565.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241565 none CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 170, 150, 115, 99, 115, 63, 99, 28, 63, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 170, 170, 150, 150, 115, 115, 115, 115, 99, 99, 99, 28, 28, 1] 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]) total number of confs: 832 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: REAL300025241565 none CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 2, 8, 10, 17, 17, 26, 26, 40, 40, 69, 109, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 2, 8, 8, 10, 10, 17, 17, 17, 17, 26, 26, 26, 69, 69, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 518 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241565 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241565 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241565/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241565 Building REAL300025241566 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241566' /scratch/stefan/7787021/working/building/REAL300025241566 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241566 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241566/0 /scratch/stefan/7787021/working/building/REAL300025241566 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/441 `/scratch/stefan/7787021/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241566.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241566 none CSCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 14, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 105, 105, 105, 101, 90, 77, 69, 77, 65, 69, 31, 64, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 157, 157, 157, 157, 105, 101, 101, 90, 90, 77, 77, 77, 77, 69, 69, 69, 31, 31, 1] 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]) total number of confs: 780 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241566 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241566 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241566/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241566 Building REAL300025241567 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241567' /scratch/stefan/7787021/working/building/REAL300025241567 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241567 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241567/0 /scratch/stefan/7787021/working/building/REAL300025241567 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/442 `/scratch/stefan/7787021/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241567.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241567 none CC(C)CCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 89, 89, 89, 89, 83, 82, 82, 82, 60, 82, 26, 59, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 191, 191, 89, 89, 89, 83, 83, 82, 82, 82, 82, 82, 82, 82, 26, 26, 1] 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]) total number of confs: 805 number of broken/clashed sets: 142 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241567 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241567 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241567/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241567 Building REAL300025241568 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241568' /scratch/stefan/7787021/working/building/REAL300025241568 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241568 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241568/0 /scratch/stefan/7787021/working/building/REAL300025241568 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/443 `/scratch/stefan/7787021/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CSC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241568.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241568 none CC(CCNC(=O)C1=CSC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 14, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 81, 95, 107, 116, 118, 118, 118, 201, 201, 201, 201, 66, 81, 27, 65, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 107, 107, 116, 116, 118, 201, 201, 201, 81, 81, 81, 27, 27, 1] 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]) total number of confs: 633 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: REAL300025241568 none CC(CCNC(=O)C1=CSC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 14, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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] 0 hydrogens 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, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 23, 27, 27, 33, 33, 68, 115, 201, 201, 201, 201, 201, 23, 23, 23, 23, 15, 15, 12, 12, 5, 1, 1, 1, 27, 27, 27, 68, 68, 201] 201 rigid atoms, others: [33, 34, 35, 5, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 543 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241568 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241568 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241568/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241568 Building REAL300025241569 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241569' /scratch/stefan/7787021/working/building/REAL300025241569 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241569 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241569/0 /scratch/stefan/7787021/working/building/REAL300025241569 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/444 `/scratch/stefan/7787021/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=CO1) `REAL300025241569.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241569 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 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, 123, 123, 123, 123, 117, 103, 84, 103, 63, 84, 26, 62, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 123, 123, 123, 117, 117, 103, 103, 103, 103, 84, 84, 84, 26, 26, 1, 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]) total number of confs: 635 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: REAL300025241569 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 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, 6, 6, 6, 12, 13, 22, 22, 28, 28, 36, 36, 72, 121, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 6, 12, 12, 14, 14, 22, 22, 22, 22, 28, 28, 28, 72, 72, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 43, 44, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 543 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241569 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241569 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241569/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241569 Building REAL300025241570 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241570' /scratch/stefan/7787021/working/building/REAL300025241570 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241570 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241570/0 /scratch/stefan/7787021/working/building/REAL300025241570 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/445 `/scratch/stefan/7787021/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1C=CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241570.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241570 none CC(CCNC(=O)CC1C=CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [93, 93, 93, 101, 109, 109, 109, 109, 197, 201, 201, 201, 201, 80, 93, 31, 80, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 101, 101, 109, 109, 109, 197, 197, 201, 201, 201, 201, 201, 201, 201, 93, 93, 93, 31, 31, 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: 772 number of broken/clashed sets: 129 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241570 none CC(CCNC(=O)CC1C=CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [27, 25, 22, 17, 17, 5, 17, 1, 1, 1, 1, 1, 1, 27, 27, 27, 29, 29, 65, 110, 201, 201, 201, 201, 201, 27, 27, 27, 27, 25, 25, 22, 22, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 65, 65, 201] 201 rigid atoms, others: [36, 37, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 519 number of broken/clashed sets: 129 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241570 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241570 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241570/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241570 Building REAL300025241571 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241571' /scratch/stefan/7787021/working/building/REAL300025241571 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241571 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241571/0 /scratch/stefan/7787021/working/building/REAL300025241571 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/446 `/scratch/stefan/7787021/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CN1C=NN=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241571.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241571 none CC(CCNC(=O)CN1C=NN=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 5, 8, 1, 8, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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] 0 hydrogens 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, 90, 104, 112, 112, 112, 201, 201, 201, 201, 201, 71, 83, 30, 70, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 90, 90, 104, 104, 112, 201, 201, 201, 83, 83, 83, 30, 30, 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: 847 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: REAL300025241571 none CC(CCNC(=O)CN1C=NN=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 5, 8, 1, 8, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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] 0 hydrogens 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, 20, 13, 13, 6, 13, 1, 1, 1, 1, 1, 1, 26, 26, 26, 32, 32, 64, 103, 201, 201, 201, 201, 201, 26, 26, 26, 26, 25, 25, 20, 20, 13, 6, 6, 1, 26, 26, 26, 64, 64, 201] 201 rigid atoms, others: [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, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 523 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241571 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241571 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241571/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241571 Building REAL300025241572 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241572' /scratch/stefan/7787021/working/building/REAL300025241572 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241572 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241572/0 /scratch/stefan/7787021/working/building/REAL300025241572 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/447 `/scratch/stefan/7787021/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CN1CCCC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241572.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241572 none CC(CCNC(=O)CN1CCCC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 90, 94, 122, 144, 155, 155, 155, 175, 201, 201, 201, 201, 201, 79, 90, 31, 78, 13, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 122, 122, 144, 144, 155, 175, 175, 201, 201, 201, 201, 201, 201, 90, 90, 90, 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: 787 number of broken/clashed sets: 115 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241572 none CC(CCNC(=O)CN1CCCC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 11, 11, 4, 11, 1, 1, 1, 1, 1, 1, 1, 25, 27, 27, 30, 30, 60, 98, 201, 201, 201, 201, 201, 25, 25, 25, 25, 24, 24, 20, 20, 11, 4, 4, 1, 1, 1, 1, 1, 1, 27, 27, 27, 60, 60, 201] 201 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 13, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 505 number of broken/clashed sets: 115 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241572 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241572 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241572/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241572 Building REAL300025241573 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241573' /scratch/stefan/7787021/working/building/REAL300025241573 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241573 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241573/0 /scratch/stefan/7787021/working/building/REAL300025241573 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/448 `/scratch/stefan/7787021/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CN(C)N=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241573.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241573 none CC(CCNC(=O)C1=CN(C)N=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 1, 8, 5, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [141, 119, 141, 162, 172, 176, 176, 176, 201, 201, 201, 201, 201, 88, 119, 31, 88, 13, 1, 1, 1, 1, 1, 1, 1, 141, 141, 141, 141, 162, 162, 172, 172, 176, 201, 201, 201, 201, 201, 119, 119, 119, 31, 31, 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: 741 number of broken/clashed sets: 105 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241573 none CC(CCNC(=O)C1=CN(C)N=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 1, 8, 5, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [22, 16, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 22, 29, 29, 36, 36, 77, 117, 201, 201, 201, 201, 201, 22, 22, 22, 22, 17, 17, 13, 13, 5, 1, 2, 2, 2, 1, 29, 29, 29, 77, 77, 201] 201 rigid atoms, others: [34, 5, 38, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 553 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241573 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241573 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241573/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241573 Building REAL300025241574 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241574' /scratch/stefan/7787021/working/building/REAL300025241574 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241574 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241574/0 /scratch/stefan/7787021/working/building/REAL300025241574 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/449 `/scratch/stefan/7787021/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C)=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241574.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241574 none CC1=NOC(C)=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 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, 7] 0 hydrogens need 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, 87, 87, 87, 86, 82, 78, 72, 78, 58, 72, 25, 57, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 87, 86, 86, 82, 82, 78, 78, 78, 78, 72, 72, 72, 25, 25, 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: 491 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: REAL300025241574 none CC1=NOC(C)=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations 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, 15, 20, 20, 22, 22, 29, 29, 67, 103, 201, 201, 201, 201, 201, 2, 2, 2, 2, 2, 2, 10, 14, 14, 16, 16, 20, 20, 20, 20, 22, 22, 22, 67, 67, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 521 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241574 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241574 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241574/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241574 Building REAL300025241575 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241575' /scratch/stefan/7787021/working/building/REAL300025241575 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241575 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241575/0 /scratch/stefan/7787021/working/building/REAL300025241575 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/450 `/scratch/stefan/7787021/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)SN=N1) `REAL300025241575.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241575 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)SN=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 7] 0 hydrogens need 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, 129, 129, 129, 128, 113, 93, 83, 93, 63, 83, 27, 63, 11, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 129, 128, 128, 113, 113, 93, 93, 93, 93, 83, 83, 83, 27, 27, 1] 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]) total number of confs: 681 number of broken/clashed sets: 105 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241575 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)SN=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations 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, 14, 25, 25, 31, 31, 42, 42, 82, 130, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 5, 11, 11, 14, 14, 25, 25, 25, 25, 31, 31, 31, 82, 82, 201] 201 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 582 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241575 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241575 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241575/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241575 Building REAL300025241576 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241576' /scratch/stefan/7787021/working/building/REAL300025241576 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241576 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241576/0 /scratch/stefan/7787021/working/building/REAL300025241576 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/451 `/scratch/stefan/7787021/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C(C)O1) `REAL300025241576.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241576 none CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C(C)O1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 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, 201, 201, 183, 183, 183, 176, 157, 128, 108, 128, 76, 108, 30, 75, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 183, 176, 176, 157, 157, 128, 128, 128, 128, 108, 108, 108, 30, 30, 1, 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]) total number of confs: 787 number of broken/clashed sets: 98 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241576 none CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C(C)O1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 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: [1, 1, 1, 1, 1, 3, 3, 3, 10, 12, 18, 18, 25, 25, 33, 33, 68, 105, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 3, 10, 10, 14, 14, 18, 18, 18, 18, 25, 25, 25, 68, 68, 201, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 540 number of broken/clashed sets: 98 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241576 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241576 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241576/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241576 Building REAL300025241577 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241577' /scratch/stefan/7787021/working/building/REAL300025241577 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241577 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241577/0 /scratch/stefan/7787021/working/building/REAL300025241577 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/452 `/scratch/stefan/7787021/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CC=CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241577.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241577 none CC(CCNC(=O)C1CC=CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [91, 85, 91, 94, 99, 100, 100, 100, 201, 201, 201, 201, 201, 65, 85, 26, 65, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 94, 94, 99, 99, 100, 201, 201, 201, 201, 201, 201, 201, 201, 201, 85, 85, 85, 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: 684 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: REAL300025241577 none CC(CCNC(=O)C1CC=CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [27, 20, 16, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 27, 30, 30, 35, 35, 69, 111, 201, 201, 201, 201, 201, 27, 27, 27, 27, 20, 20, 16, 16, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 69, 69, 201] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 533 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241577 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241577 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241577/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241577 Building REAL300025241578 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241578' /scratch/stefan/7787021/working/building/REAL300025241578 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241578 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241578/0 /scratch/stefan/7787021/working/building/REAL300025241578 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/453 `/scratch/stefan/7787021/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1) `REAL300025241578.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241578 none CC1=NOC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 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: [201, 201, 201, 201, 193, 193, 193, 172, 150, 116, 99, 116, 63, 99, 28, 63, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 193, 172, 172, 150, 150, 116, 116, 116, 116, 99, 99, 99, 28, 28, 1, 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]) total number of confs: 823 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241578 none CC1=NOC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 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, 1, 1, 2, 2, 3, 8, 10, 17, 17, 24, 24, 34, 34, 61, 101, 201, 201, 201, 201, 201, 1, 2, 2, 2, 3, 8, 8, 10, 10, 17, 17, 17, 17, 24, 24, 24, 61, 61, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 502 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241578 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241578 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241578/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241578 Building REAL300025241579 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241579' /scratch/stefan/7787021/working/building/REAL300025241579 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241579 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241579/0 /scratch/stefan/7787021/working/building/REAL300025241579 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/454 `/scratch/stefan/7787021/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241579.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241579 none CC(CCNC(=O)C1=CC=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 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: [121, 104, 121, 157, 178, 190, 190, 190, 201, 201, 201, 201, 71, 104, 28, 70, 13, 1, 1, 1, 1, 1, 1, 1, 121, 121, 121, 121, 157, 157, 178, 178, 190, 201, 201, 201, 201, 104, 104, 104, 28, 28, 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: 802 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241579 none CC(CCNC(=O)C1=CC=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 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, 10, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 17, 24, 24, 31, 31, 60, 100, 201, 201, 201, 201, 201, 17, 17, 17, 17, 12, 12, 10, 10, 3, 1, 1, 1, 1, 24, 24, 24, 60, 60, 201] 201 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 497 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241579 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241579 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241579/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241579 Building REAL300025241580 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241580' /scratch/stefan/7787021/working/building/REAL300025241580 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241580 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241580/0 /scratch/stefan/7787021/working/building/REAL300025241580 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/455 `/scratch/stefan/7787021/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC(Cl)=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241580.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241580 none CC(CCNC(=O)C1=CC(Cl)=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 16, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 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: [122, 105, 122, 154, 175, 191, 191, 191, 201, 201, 201, 201, 201, 73, 105, 30, 72, 13, 1, 1, 1, 1, 1, 1, 1, 122, 122, 122, 122, 154, 154, 175, 175, 191, 201, 201, 201, 105, 105, 105, 30, 30, 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: 792 number of broken/clashed sets: 84 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241580 none CC(CCNC(=O)C1=CC(Cl)=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 16, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 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, 12, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 17, 24, 24, 34, 34, 65, 105, 201, 201, 201, 201, 201, 17, 17, 17, 17, 13, 13, 12, 12, 4, 1, 1, 1, 24, 24, 24, 65, 65, 201] 201 rigid atoms, others: [34, 35, 36, 5, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 504 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241580 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241580 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241580/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241580 Building REAL300025241581 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241581' /scratch/stefan/7787021/working/building/REAL300025241581 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241581 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241581/0 /scratch/stefan/7787021/working/building/REAL300025241581 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/456 `/scratch/stefan/7787021/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)CCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241581.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241581 none CC(=O)CCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 201, 199, 186, 68, 68, 68, 65, 65, 44, 44, 44, 33, 44, 25, 33, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 199, 199, 199, 199, 186, 186, 68, 65, 65, 65, 65, 44, 44, 44, 44, 44, 44, 44, 25, 25, 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: 831 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241581 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241581 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241581/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241581 Building REAL300025241582 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241582' /scratch/stefan/7787021/working/building/REAL300025241582 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241582 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241582/0 /scratch/stefan/7787021/working/building/REAL300025241582 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/457 `/scratch/stefan/7787021/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)N1C) `REAL300025241582.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241582 none CC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)N1C 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 116, 116, 116, 115, 105, 87, 75, 87, 53, 75, 24, 53, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 116, 115, 115, 105, 105, 87, 87, 87, 87, 75, 75, 75, 24, 24, 1, 201, 201, 201] 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]) total number of confs: 628 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241582 none CC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)N1C 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 5, 8, 11, 17, 17, 21, 21, 31, 31, 65, 103, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 5, 8, 8, 11, 11, 17, 17, 17, 17, 21, 21, 21, 65, 65, 201, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 535 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241582 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241582 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241582/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241582 Building REAL300025241583 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241583' /scratch/stefan/7787021/working/building/REAL300025241583 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241583 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241583/0 /scratch/stefan/7787021/working/building/REAL300025241583 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/458 `/scratch/stefan/7787021/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=COC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241583.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241583 none CC(CCNC(=O)C1=COC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 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] 0 hydrogens 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, 99, 117, 130, 138, 141, 141, 141, 201, 201, 201, 201, 76, 99, 32, 76, 13, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 130, 130, 138, 138, 141, 201, 201, 201, 99, 99, 99, 32, 32, 1] 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]) total number of confs: 665 number of broken/clashed sets: 101 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241583 none CC(CCNC(=O)C1=COC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 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] 0 hydrogens 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, 13, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 20, 25, 25, 31, 31, 69, 119, 201, 201, 201, 201, 201, 20, 20, 20, 20, 14, 14, 11, 11, 5, 1, 1, 1, 25, 25, 25, 69, 69, 201] 201 rigid atoms, others: [33, 34, 35, 5, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 535 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241583 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241583 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241583/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241583 Building REAL300025241584 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241584' /scratch/stefan/7787021/working/building/REAL300025241584 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241584 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241584/0 /scratch/stefan/7787021/working/building/REAL300025241584 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/459 `/scratch/stefan/7787021/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CN1C=CC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241584.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241584 none CC(CCNC(=O)CN1C=CC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 8, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [69, 66, 69, 88, 113, 121, 121, 121, 201, 201, 201, 201, 201, 57, 66, 28, 56, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 88, 88, 113, 113, 121, 201, 201, 201, 201, 201, 66, 66, 66, 28, 28, 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: 915 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: REAL300025241584 none CC(CCNC(=O)CN1C=CC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 8, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [29, 23, 18, 11, 11, 5, 11, 1, 1, 1, 1, 1, 1, 29, 32, 32, 38, 38, 79, 114, 201, 201, 201, 201, 201, 29, 29, 29, 29, 23, 23, 18, 18, 11, 5, 5, 1, 1, 1, 32, 32, 32, 79, 79, 201] 201 rigid atoms, others: [36, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 581 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241584 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241584 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241584/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241584 Building REAL300025241585 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241585' /scratch/stefan/7787021/working/building/REAL300025241585 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241585 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241585/0 /scratch/stefan/7787021/working/building/REAL300025241585 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/460 `/scratch/stefan/7787021/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)OC=C1) `REAL300025241585.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241585 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)OC=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 145, 145, 145, 141, 124, 95, 80, 95, 56, 80, 26, 56, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 145, 141, 141, 124, 124, 95, 95, 95, 95, 80, 80, 80, 26, 26, 1, 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]) total number of confs: 728 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: REAL300025241585 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)OC=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 13, 23, 23, 29, 29, 44, 44, 84, 124, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 3, 8, 8, 13, 13, 23, 23, 23, 23, 29, 29, 29, 84, 84, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 43, 44, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 593 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241585 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241585 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241585/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241585 Building REAL300025241586 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241586' /scratch/stefan/7787021/working/building/REAL300025241586 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241586 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241586/0 /scratch/stefan/7787021/working/building/REAL300025241586 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/461 `/scratch/stefan/7787021/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CC2CCC1C2)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241586.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241586 none CC(CCNC(=O)C1CC2CCC1C2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 131, 154, 179, 199, 201, 201, 201, 201, 201, 201, 201, 201, 201, 81, 131, 30, 81, 13, 1, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 179, 179, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 131, 131, 131, 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: 792 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241586 none CC(CCNC(=O)C1CC2CCC1C2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 9, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 15, 22, 22, 36, 36, 64, 102, 201, 201, 201, 201, 201, 15, 15, 15, 15, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 64, 64, 201] 201 rigid atoms, others: [45, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 43, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 46, 47, 48, 49, 50, 51]) total number of confs: 505 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241586 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241586 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241586/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241586 Building REAL300025241587 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241587' /scratch/stefan/7787021/working/building/REAL300025241587 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241587 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241587/0 /scratch/stefan/7787021/working/building/REAL300025241587 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/462 `/scratch/stefan/7787021/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=C(Cl)O1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241587.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241587 none CC(CCNC(=O)C1=CC=C(Cl)O1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 1, 1, 1, 1, 16, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 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: [122, 104, 122, 156, 177, 201, 201, 201, 201, 201, 201, 201, 201, 62, 104, 27, 61, 13, 1, 1, 1, 1, 1, 1, 1, 122, 122, 122, 122, 156, 156, 177, 177, 201, 201, 201, 104, 104, 104, 27, 27, 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: 821 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241587 none CC(CCNC(=O)C1=CC=C(Cl)O1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 1, 1, 1, 1, 16, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 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, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 22, 22, 34, 34, 62, 102, 201, 201, 201, 201, 201, 14, 14, 14, 14, 8, 8, 6, 6, 2, 1, 1, 22, 22, 22, 62, 62, 201] 201 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 503 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241587 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241587 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241587/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241587 Building REAL300025241588 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241588' /scratch/stefan/7787021/working/building/REAL300025241588 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241588 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241588/0 /scratch/stefan/7787021/working/building/REAL300025241588 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/463 `/scratch/stefan/7787021/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=NN1C) `REAL300025241588.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241588 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 101, 101, 101, 100, 93, 81, 71, 81, 53, 71, 23, 53, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 101, 100, 100, 93, 93, 81, 81, 81, 81, 71, 71, 71, 23, 23, 1, 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]) total number of confs: 562 number of broken/clashed sets: 99 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241588 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 15, 19, 19, 23, 23, 32, 32, 65, 104, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 15, 15, 19, 19, 19, 19, 23, 23, 23, 65, 65, 201, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 44, 22, 23, 24, 25] set([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, 45, 46, 47]) total number of confs: 524 number of broken/clashed sets: 99 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241588 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241588 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241588/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241588 Building REAL300025241589 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241589' /scratch/stefan/7787021/working/building/REAL300025241589 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241589 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241589/0 /scratch/stefan/7787021/working/building/REAL300025241589 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/464 `/scratch/stefan/7787021/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241589.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241589 none CCCCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 189, 52, 52, 52, 52, 52, 41, 40, 41, 31, 41, 24, 31, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 189, 189, 52, 52, 52, 52, 52, 41, 41, 41, 41, 41, 41, 41, 24, 24, 1] 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]) total number of confs: 836 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241589 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241589 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241589/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241589 Building REAL300025241590 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241590' /scratch/stefan/7787021/working/building/REAL300025241590 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241590 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241590/0 /scratch/stefan/7787021/working/building/REAL300025241590 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/465 `/scratch/stefan/7787021/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC(C)(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241590.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241590 none CC(CCNC(=O)CC(C)(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 81, 96, 112, 126, 132, 132, 132, 201, 201, 201, 201, 59, 81, 27, 58, 13, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 112, 112, 126, 126, 132, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 81, 81, 81, 27, 27, 1] 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]) total number of confs: 943 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241590 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241590 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241590/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241590 Building REAL300025241591 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241591' /scratch/stefan/7787021/working/building/REAL300025241591 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241591 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241591/0 /scratch/stefan/7787021/working/building/REAL300025241591 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/466 `/scratch/stefan/7787021/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=N1) `REAL300025241591.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241591 none CC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 170, 170, 170, 158, 154, 117, 76, 117, 63, 76, 37, 63, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 170, 158, 158, 154, 154, 117, 117, 117, 117, 76, 76, 76, 37, 37, 1, 201] 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]) total number of confs: 823 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241591 none CC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 5, 16, 19, 23, 23, 28, 28, 56, 56, 82, 121, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 5, 16, 16, 19, 19, 23, 23, 23, 23, 28, 28, 28, 82, 82, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 567 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241591 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241591 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241591/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241591 Building REAL300025241592 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241592' /scratch/stefan/7787021/working/building/REAL300025241592 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241592 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241592/0 /scratch/stefan/7787021/working/building/REAL300025241592 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/467 `/scratch/stefan/7787021/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=CN1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241592.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241592 none CC(CCNC(=O)C1=CC=CN1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [125, 108, 125, 156, 175, 184, 184, 184, 201, 201, 201, 201, 201, 74, 108, 28, 73, 13, 1, 1, 1, 1, 1, 1, 1, 125, 125, 125, 125, 156, 156, 175, 175, 184, 201, 201, 201, 201, 201, 201, 108, 108, 108, 28, 28, 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: 768 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: REAL300025241592 none CC(CCNC(=O)C1=CC=CN1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [15, 10, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 15, 22, 22, 31, 31, 66, 104, 201, 201, 201, 201, 201, 15, 15, 15, 15, 10, 10, 9, 9, 4, 1, 1, 1, 2, 2, 2, 22, 22, 22, 66, 66, 201] 201 rigid atoms, others: [34, 35, 36, 5, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 522 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241592 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241592 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241592/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241592 Building REAL300025241593 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241593' /scratch/stefan/7787021/working/building/REAL300025241593 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241593 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241593/0 /scratch/stefan/7787021/working/building/REAL300025241593 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/468 `/scratch/stefan/7787021/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCN1C=NC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241593.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241593 none CC(CCNC(=O)CCN1C=NC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [69, 69, 69, 73, 94, 95, 95, 95, 188, 188, 201, 201, 201, 201, 59, 69, 27, 59, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 73, 73, 94, 94, 95, 188, 188, 188, 188, 201, 201, 69, 69, 69, 27, 27, 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: 839 number of broken/clashed sets: 108 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241593 none CC(CCNC(=O)CCN1C=NC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [25, 24, 18, 12, 12, 7, 12, 5, 1, 1, 1, 1, 1, 1, 25, 25, 25, 31, 31, 67, 106, 201, 201, 201, 201, 201, 25, 25, 25, 25, 24, 24, 18, 18, 12, 7, 7, 5, 5, 1, 1, 25, 25, 25, 67, 67, 201] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 551 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241593 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241593 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241593/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241593 Building REAL300025241594 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241594' /scratch/stefan/7787021/working/building/REAL300025241594 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241594 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241594/0 /scratch/stefan/7787021/working/building/REAL300025241594 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/469 `/scratch/stefan/7787021/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241594.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241594 none CCCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 82, 82, 82, 82, 75, 73, 73, 73, 55, 73, 25, 54, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 185, 185, 82, 82, 82, 75, 75, 73, 73, 73, 73, 73, 73, 73, 25, 25, 1] 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]) total number of confs: 830 number of broken/clashed sets: 139 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241594 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241594 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241594/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241594 Building REAL300025241595 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241595' /scratch/stefan/7787021/working/building/REAL300025241595 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241595 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241595/0 /scratch/stefan/7787021/working/building/REAL300025241595 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/470 `/scratch/stefan/7787021/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=N1) `REAL300025241595.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241595 none CC1=CC=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=N1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 183, 159, 123, 110, 123, 64, 110, 27, 64, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 183, 183, 159, 159, 123, 123, 123, 123, 110, 110, 110, 27, 27, 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: 843 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: REAL300025241595 none CC1=CC=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=N1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 2, 2, 2, 8, 9, 16, 16, 26, 26, 36, 36, 68, 106, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 2, 8, 8, 10, 10, 16, 16, 16, 16, 26, 26, 26, 68, 68, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 29, 30, 31] set([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]) total number of confs: 525 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241595 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241595 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241595/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241595 Building REAL300025241596 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241596' /scratch/stefan/7787021/working/building/REAL300025241596 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241596 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241596/0 /scratch/stefan/7787021/working/building/REAL300025241596 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/471 `/scratch/stefan/7787021/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241596.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241596 none CC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 201, 199, 199, 182, 182, 131, 100, 131, 67, 100, 30, 66, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 199, 182, 182, 182, 182, 131, 131, 131, 131, 100, 100, 100, 30, 30, 1] 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]) total number of confs: 874 number of broken/clashed sets: 127 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241596 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241596 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241596/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241596 Building REAL300025241597 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241597' /scratch/stefan/7787021/working/building/REAL300025241597 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241597 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241597/0 /scratch/stefan/7787021/working/building/REAL300025241597 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/472 `/scratch/stefan/7787021/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCN1C=CC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241597.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241597 none CC(CCNC(=O)CCN1C=CC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [50, 45, 50, 62, 74, 103, 103, 103, 190, 190, 201, 201, 201, 201, 39, 45, 23, 38, 13, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 62, 62, 74, 74, 103, 190, 190, 190, 190, 201, 201, 201, 45, 45, 45, 23, 23, 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: 810 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: REAL300025241597 none CC(CCNC(=O)CCN1C=CC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [32, 27, 23, 12, 12, 7, 12, 5, 1, 1, 1, 1, 1, 1, 32, 35, 35, 39, 39, 78, 110, 201, 201, 201, 201, 201, 32, 32, 32, 32, 27, 27, 23, 23, 12, 7, 7, 5, 5, 1, 1, 1, 35, 35, 35, 78, 78, 201] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46, 47]) total number of confs: 579 number of broken/clashed sets: 126 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241597 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241597 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241597/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241597 Building REAL300025241598 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241598' /scratch/stefan/7787021/working/building/REAL300025241598 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241598 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241598/0 /scratch/stefan/7787021/working/building/REAL300025241598 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/473 `/scratch/stefan/7787021/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=CC=C1O)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241598.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241598 none CC(CCNC(=O)C1=CC=CC=C1O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [122, 108, 122, 149, 168, 174, 174, 174, 201, 201, 201, 201, 201, 201, 75, 108, 29, 75, 13, 1, 1, 1, 1, 1, 1, 1, 122, 122, 122, 122, 149, 149, 168, 168, 174, 201, 201, 201, 201, 402, 108, 108, 108, 29, 29, 1] 402 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: 1146 number of broken/clashed sets: 224 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241598 none CC(CCNC(=O)C1=CC=CC=C1O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [15, 10, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 15, 20, 20, 28, 28, 58, 96, 201, 201, 201, 201, 201, 15, 15, 15, 15, 12, 12, 11, 11, 4, 1, 1, 1, 1, 2, 20, 20, 20, 58, 58, 201] 402 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 506 number of broken/clashed sets: 224 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241598 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241598 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241598/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241598 Building REAL300025241599 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241599' /scratch/stefan/7787021/working/building/REAL300025241599 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241599 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241599/0 /scratch/stefan/7787021/working/building/REAL300025241599 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/474 `/scratch/stefan/7787021/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241599.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241599 none CCC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 201, 131, 131, 131, 125, 112, 98, 112, 71, 98, 29, 70, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 131, 131, 131, 125, 125, 112, 112, 112, 112, 98, 98, 98, 29, 29, 1] 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]) total number of confs: 885 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241599 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241599 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241599/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241599 Building REAL300025241600 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241600' /scratch/stefan/7787021/working/building/REAL300025241600 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241600 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241600/0 /scratch/stefan/7787021/working/building/REAL300025241600 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/475 `/scratch/stefan/7787021/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)SCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241600.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241600 none CC(C)SCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 194, 110, 110, 110, 107, 90, 74, 73, 74, 54, 73, 27, 53, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 194, 194, 110, 107, 107, 90, 90, 74, 74, 74, 74, 73, 73, 73, 27, 27, 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: 868 number of broken/clashed sets: 128 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241600 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241600 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241600/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241600 Building REAL300025241601 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241601' /scratch/stefan/7787021/working/building/REAL300025241601 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241601 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241601/0 /scratch/stefan/7787021/working/building/REAL300025241601 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/476 `/scratch/stefan/7787021/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241601.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241601 none CC(=O)N(C)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 6, 7, 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, 7, 7, 7] 0 hydrogens need 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, 172, 201, 157, 157, 157, 142, 139, 117, 97, 117, 71, 97, 28, 70, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 172, 172, 157, 142, 142, 139, 139, 117, 117, 117, 117, 97, 97, 97, 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: 833 number of broken/clashed sets: 110 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241601 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241601 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241601/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241601 Building REAL300025241602 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241602' /scratch/stefan/7787021/working/building/REAL300025241602 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241602 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241602/0 /scratch/stefan/7787021/working/building/REAL300025241602 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/477 `/scratch/stefan/7787021/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241602.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241602 none CCC(CC)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 189, 199, 201, 189, 189, 181, 169, 144, 122, 144, 85, 122, 30, 85, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 199, 201, 201, 201, 201, 201, 189, 181, 181, 169, 169, 144, 144, 144, 144, 122, 122, 122, 30, 30, 1] 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]) total number of confs: 820 number of broken/clashed sets: 102 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241602 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241602 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241602/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241602 Building REAL300025241603 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241603' /scratch/stefan/7787021/working/building/REAL300025241603 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241603 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241603/0 /scratch/stefan/7787021/working/building/REAL300025241603 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/478 `/scratch/stefan/7787021/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241603.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241603 none CC(C)OCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 193, 105, 105, 105, 98, 98, 65, 65, 65, 48, 65, 31, 48, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 193, 193, 193, 193, 105, 98, 98, 98, 98, 65, 65, 65, 65, 65, 65, 65, 31, 31, 1] 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]) total number of confs: 852 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241603 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241603 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241603/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241603 Building REAL300025241604 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241604' /scratch/stefan/7787021/working/building/REAL300025241604 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241604 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241604/0 /scratch/stefan/7787021/working/building/REAL300025241604 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/479 `/scratch/stefan/7787021/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NNC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1) `REAL300025241604.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241604 none CCC1=NNC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 113, 113, 113, 113, 110, 110, 110, 94, 92, 70, 57, 70, 46, 58, 33, 46, 12, 1, 1, 1, 1, 1, 1, 1, 113, 201, 201, 201, 201, 201, 113, 110, 94, 94, 92, 92, 70, 70, 70, 70, 58, 58, 58, 33, 33, 1, 113] 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]) total number of confs: 1014 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: REAL300025241604 none CCC1=NNC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 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, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 9, 9, 12, 12, 16, 16, 28, 28, 37, 56, 113, 113, 113, 113, 113, 1, 6, 6, 6, 6, 6, 1, 3, 9, 9, 9, 9, 12, 12, 12, 12, 16, 16, 16, 37, 37, 113, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 47, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 299 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241604 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241604 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241604/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241604 Building REAL300025241605 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241605' /scratch/stefan/7787021/working/building/REAL300025241605 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241605 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241605/0 /scratch/stefan/7787021/working/building/REAL300025241605 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/480 `/scratch/stefan/7787021/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1CCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241605.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241605 none CC(CCNC(=O)CCC1CCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 51, 69, 80, 88, 88, 88, 189, 201, 201, 201, 201, 201, 42, 44, 25, 41, 13, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 69, 69, 80, 80, 88, 189, 189, 201, 201, 201, 201, 201, 201, 201, 201, 201, 44, 44, 44, 25, 25, 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: 857 number of broken/clashed sets: 149 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241605 none CC(CCNC(=O)CCC1CCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 15, 15, 6, 15, 4, 1, 1, 1, 1, 1, 1, 33, 36, 36, 38, 38, 74, 110, 201, 201, 201, 201, 201, 33, 33, 33, 33, 28, 28, 23, 23, 15, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 74, 74, 201] 201 rigid atoms, others: [45, 43, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 49, 50, 51]) total number of confs: 568 number of broken/clashed sets: 149 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241605 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241605 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241605/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241605 Building REAL300025241606 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241606' /scratch/stefan/7787021/working/building/REAL300025241606 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241606 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241606/0 /scratch/stefan/7787021/working/building/REAL300025241606 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/481 `/scratch/stefan/7787021/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1COCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241606.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241606 none CC(CCNC(=O)C1COCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 93, 113, 145, 165, 170, 170, 170, 201, 201, 201, 201, 201, 62, 93, 27, 61, 12, 1, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 145, 145, 165, 165, 170, 201, 201, 201, 201, 201, 201, 201, 93, 93, 93, 27, 27, 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: 842 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241606 none CC(CCNC(=O)C1COCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 24, 29, 29, 40, 40, 80, 123, 201, 201, 201, 201, 201, 24, 24, 24, 24, 18, 18, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 80, 80, 201] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46]) total number of confs: 579 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241606 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241606 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241606/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241606 Building REAL300025241607 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241607' /scratch/stefan/7787021/working/building/REAL300025241607 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241607 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241607/0 /scratch/stefan/7787021/working/building/REAL300025241607 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/482 `/scratch/stefan/7787021/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=NN1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241607.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241607 none CC(CCNC(=O)C1=CC=NN1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 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: [128, 106, 128, 162, 180, 193, 193, 193, 201, 201, 201, 201, 75, 106, 29, 74, 13, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 128, 162, 162, 180, 180, 193, 201, 201, 201, 106, 106, 106, 29, 29, 1] 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]) total number of confs: 814 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241607 none CC(CCNC(=O)C1=CC=NN1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 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: [18, 12, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 18, 26, 26, 37, 37, 69, 106, 201, 201, 201, 201, 201, 18, 18, 18, 18, 14, 14, 11, 11, 4, 1, 1, 1, 26, 26, 26, 69, 69, 201] 201 rigid atoms, others: [33, 34, 35, 5, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 524 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241607 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241607 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241607/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241607 Building REAL300025241608 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241608' /scratch/stefan/7787021/working/building/REAL300025241608 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241608 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241608/0 /scratch/stefan/7787021/working/building/REAL300025241608 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/483 `/scratch/stefan/7787021/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C(C)N1C=CC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241608.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241608 none CC(CCNC(=O)C(C)N1C=CC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [76, 70, 76, 93, 107, 139, 139, 139, 201, 201, 201, 201, 201, 201, 60, 70, 29, 59, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 93, 93, 107, 107, 139, 201, 201, 201, 201, 201, 201, 201, 70, 70, 70, 29, 29, 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: 901 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: REAL300025241608 none CC(CCNC(=O)C(C)N1C=CC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [28, 22, 18, 8, 8, 6, 8, 1, 6, 1, 1, 1, 1, 1, 28, 30, 30, 35, 35, 76, 112, 201, 201, 201, 201, 201, 28, 28, 28, 28, 22, 22, 18, 18, 8, 6, 6, 6, 6, 1, 1, 1, 30, 30, 30, 76, 76, 201] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 41, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46, 47]) total number of confs: 575 number of broken/clashed sets: 109 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241608 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241608 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241608/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241608 Building REAL300025241609 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241609' /scratch/stefan/7787021/working/building/REAL300025241609 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241609 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241609/0 /scratch/stefan/7787021/working/building/REAL300025241609 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/484 `/scratch/stefan/7787021/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(CC)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241609.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241609 none CCCCC(CC)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 156, 93, 156, 156, 93, 93, 83, 83, 52, 47, 52, 37, 48, 24, 37, 11, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 156, 156, 156, 156, 156, 156, 93, 83, 83, 83, 83, 52, 52, 52, 52, 48, 48, 48, 24, 24, 1] 201 rigid atoms, others: [55, 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, 51, 52, 53, 54]) total number of confs: 990 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241609 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241609 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241609/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241609 Building REAL300025241610 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241610' /scratch/stefan/7787021/working/building/REAL300025241610 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241610 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241610/0 /scratch/stefan/7787021/working/building/REAL300025241610 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/485 `/scratch/stefan/7787021/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241610.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241610 none CSC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 14, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 141, 198, 141, 141, 135, 115, 94, 83, 94, 57, 83, 26, 56, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 198, 198, 198, 198, 141, 135, 135, 115, 115, 94, 94, 94, 94, 83, 83, 83, 26, 26, 1] 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]) total number of confs: 914 number of broken/clashed sets: 124 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241610 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241610 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241610/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241610 Building REAL300025241611 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241611' /scratch/stefan/7787021/working/building/REAL300025241611 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241611 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241611/0 /scratch/stefan/7787021/working/building/REAL300025241611 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/486 `/scratch/stefan/7787021/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241611.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241611 none CCOC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens need 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, 192, 201, 192, 192, 185, 163, 132, 108, 132, 72, 108, 30, 71, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 192, 185, 185, 163, 163, 132, 132, 132, 132, 108, 108, 108, 30, 30, 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: 875 number of broken/clashed sets: 99 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241611 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241611 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241611/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241611 Building REAL300025241612 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241612' /scratch/stefan/7787021/working/building/REAL300025241612 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241612 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241612/0 /scratch/stefan/7787021/working/building/REAL300025241612 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/487 `/scratch/stefan/7787021/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)COCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241612.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241612 none CC(C)COCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 200, 200, 200, 133, 133, 133, 133, 133, 83, 83, 83, 65, 83, 36, 65, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 200, 200, 133, 133, 133, 133, 133, 83, 83, 83, 83, 83, 83, 83, 36, 36, 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: 948 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241612 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241612 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241612/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241612 Building REAL300025241613 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241613' /scratch/stefan/7787021/working/building/REAL300025241613 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241613 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241613/0 /scratch/stefan/7787021/working/building/REAL300025241613 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/488 `/scratch/stefan/7787021/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241613.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241613 none CCOCCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 168, 198, 66, 66, 66, 57, 57, 40, 39, 40, 31, 40, 21, 31, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 186, 183, 201, 201, 198, 198, 66, 57, 57, 57, 57, 40, 40, 40, 40, 40, 40, 40, 21, 21, 1] 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]) total number of confs: 971 number of broken/clashed sets: 79 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241613 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241613 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241613/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241613 Building REAL300025241614 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241614' /scratch/stefan/7787021/working/building/REAL300025241614 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241614 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241614/0 /scratch/stefan/7787021/working/building/REAL300025241614 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/489 `/scratch/stefan/7787021/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)COCC1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241614.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241614 none CC(CCNC(=O)COCC1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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: [27, 27, 27, 27, 29, 32, 32, 32, 91, 128, 164, 201, 201, 21, 27, 16, 21, 12, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 29, 29, 32, 91, 91, 164, 164, 201, 201, 201, 201, 201, 27, 27, 27, 16, 16, 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: 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: REAL300025241614 none CC(CCNC(=O)COCC1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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: [68, 68, 68, 55, 55, 39, 55, 15, 6, 1, 1, 1, 1, 68, 68, 68, 86, 86, 121, 152, 201, 201, 201, 201, 201, 68, 68, 68, 68, 68, 68, 68, 68, 55, 39, 39, 6, 6, 1, 1, 1, 1, 1, 68, 68, 68, 121, 121, 201] 201 rigid atoms, others: [38, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 667 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241614 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241614 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241614/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241614 Building REAL300025241615 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241615' /scratch/stefan/7787021/working/building/REAL300025241615 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241615 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241615/0 /scratch/stefan/7787021/working/building/REAL300025241615 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/490 `/scratch/stefan/7787021/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1CCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241615.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241615 none CC(CCNC(=O)CC1CCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 71, 74, 90, 110, 119, 119, 119, 197, 201, 201, 201, 201, 62, 71, 29, 62, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 90, 90, 110, 110, 119, 197, 197, 201, 201, 201, 201, 201, 201, 201, 71, 71, 71, 29, 29, 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: 853 number of broken/clashed sets: 134 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241615 none CC(CCNC(=O)CC1CCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 25, 15, 15, 5, 15, 1, 1, 1, 1, 1, 1, 32, 35, 35, 37, 37, 79, 118, 201, 201, 201, 201, 201, 32, 32, 32, 32, 29, 29, 25, 25, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 79, 79, 201] 201 rigid atoms, others: [36, 37, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 565 number of broken/clashed sets: 134 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241615 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241615 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241615/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241615 Building REAL300025241616 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241616' /scratch/stefan/7787021/working/building/REAL300025241616 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241616 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241616/0 /scratch/stefan/7787021/working/building/REAL300025241616 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/491 `/scratch/stefan/7787021/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)SC=N1) `REAL300025241616.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241616 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)SC=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need 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, 106, 106, 106, 106, 99, 89, 78, 89, 60, 78, 26, 60, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 106, 106, 106, 99, 99, 89, 89, 89, 89, 78, 78, 78, 26, 26, 1, 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]) total number of confs: 577 number of broken/clashed sets: 93 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241616 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)SC=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 201 conformations 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, 8, 10, 12, 17, 17, 21, 21, 30, 30, 63, 101, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 8, 10, 10, 12, 12, 17, 17, 17, 17, 21, 21, 21, 63, 63, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 43, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 506 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241616 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241616 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241616/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241616 Building REAL300025241617 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241617' /scratch/stefan/7787021/working/building/REAL300025241617 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241617 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241617/0 /scratch/stefan/7787021/working/building/REAL300025241617 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/492 `/scratch/stefan/7787021/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CNN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241617.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241617 none CC(CCNC(=O)C1=CNN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 8, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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: [153, 126, 153, 181, 191, 201, 201, 201, 201, 201, 201, 201, 95, 126, 33, 94, 13, 1, 1, 1, 1, 1, 1, 1, 153, 153, 153, 153, 181, 181, 191, 191, 201, 201, 201, 201, 126, 126, 126, 33, 33, 1] 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]) total number of confs: 784 number of broken/clashed sets: 101 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241617 none CC(CCNC(=O)C1=CNN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 8, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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: [20, 13, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 20, 29, 29, 35, 35, 73, 119, 201, 201, 201, 201, 201, 20, 20, 20, 20, 15, 15, 11, 11, 3, 1, 1, 1, 29, 29, 29, 73, 73, 201] 201 rigid atoms, others: [33, 34, 35, 5, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 558 number of broken/clashed sets: 115 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241617 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241617 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241617/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241617 Building REAL300025241618 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241618' /scratch/stefan/7787021/working/building/REAL300025241618 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241618 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241618/0 /scratch/stefan/7787021/working/building/REAL300025241618 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/493 `/scratch/stefan/7787021/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CNC(=O)C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241618.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241618 none CC(CCNC(=O)CNC(=O)C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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, 7, 4, 7, 6, 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: [34, 34, 34, 34, 35, 45, 45, 45, 123, 152, 152, 152, 201, 201, 25, 34, 16, 25, 12, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 35, 35, 45, 123, 123, 152, 201, 201, 201, 201, 201, 34, 34, 34, 16, 16, 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: 769 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: REAL300025241618 none CC(CCNC(=O)CNC(=O)C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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, 7, 4, 7, 6, 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: [54, 54, 54, 49, 49, 34, 50, 11, 11, 1, 11, 1, 1, 1, 54, 54, 54, 75, 75, 122, 150, 201, 201, 201, 201, 201, 54, 54, 54, 54, 54, 54, 54, 54, 50, 34, 34, 11, 1, 1, 1, 1, 1, 54, 54, 54, 122, 122, 201] 201 rigid atoms, others: [38, 39, 40, 9, 42, 11, 12, 13, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48]) total number of confs: 664 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241618 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241618 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241618/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241618 Building REAL300025241619 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241619' /scratch/stefan/7787021/working/building/REAL300025241619 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241619 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241619/0 /scratch/stefan/7787021/working/building/REAL300025241619 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/494 `/scratch/stefan/7787021/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241619.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241619 none COCCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 195, 91, 91, 91, 80, 80, 55, 52, 55, 39, 53, 27, 39, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 191, 191, 201, 201, 195, 195, 91, 80, 80, 80, 80, 55, 55, 55, 55, 53, 53, 53, 27, 27, 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: 1015 number of broken/clashed sets: 83 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241619 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241619 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241619/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241619 Building REAL300025241620 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241620' /scratch/stefan/7787021/working/building/REAL300025241620 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241620 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241620/0 /scratch/stefan/7787021/working/building/REAL300025241620 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/495 `/scratch/stefan/7787021/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)COC1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241620.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241620 none CC(CCNC(=O)COC1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 49, 55, 71, 86, 90, 90, 90, 143, 154, 201, 201, 201, 201, 46, 49, 26, 45, 13, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 71, 71, 86, 86, 90, 143, 143, 201, 201, 201, 201, 201, 201, 201, 201, 201, 49, 49, 49, 26, 26, 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: 861 number of broken/clashed sets: 139 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241620 none CC(CCNC(=O)COC1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 30, 26, 17, 17, 9, 17, 4, 1, 1, 1, 1, 1, 1, 34, 39, 39, 41, 41, 81, 115, 201, 201, 201, 201, 201, 34, 34, 34, 34, 30, 30, 26, 26, 17, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 81, 81, 201] 201 rigid atoms, others: [45, 43, 37, 38, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 607 number of broken/clashed sets: 139 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241620 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241620 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241620/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241620 Building REAL300025241621 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241621' /scratch/stefan/7787021/working/building/REAL300025241621 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241621 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241621/0 /scratch/stefan/7787021/working/building/REAL300025241621 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/496 `/scratch/stefan/7787021/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=NC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241621.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241621 none CC1=NC=NC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 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, 3, 7, 3, 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: [201, 201, 201, 182, 201, 201, 97, 97, 97, 97, 91, 87, 83, 87, 64, 83, 25, 64, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 97, 97, 97, 91, 91, 87, 87, 87, 87, 83, 83, 83, 25, 25, 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: 611 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241621 none CC1=NC=NC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 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, 3, 7, 3, 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, 1, 1, 1, 1, 10, 10, 10, 16, 18, 23, 23, 25, 25, 32, 32, 71, 116, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 10, 16, 16, 18, 18, 23, 23, 23, 23, 25, 25, 25, 71, 71, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29, 30] set([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: 541 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241621 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241621 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241621/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241621 Building REAL300025241622 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241622' /scratch/stefan/7787021/working/building/REAL300025241622 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241622 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241622/0 /scratch/stefan/7787021/working/building/REAL300025241622 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/497 `/scratch/stefan/7787021/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241622.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241622 none CCSCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 150, 67, 67, 67, 67, 67, 59, 59, 59, 41, 59, 34, 41, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 150, 150, 150, 150, 67, 67, 67, 67, 67, 59, 59, 59, 59, 59, 59, 59, 34, 34, 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: 737 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241622 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241622 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241622/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241622 Building REAL300025241623 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241623' /scratch/stefan/7787021/working/building/REAL300025241623 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241623 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241623/0 /scratch/stefan/7787021/working/building/REAL300025241623 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/498 `/scratch/stefan/7787021/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241623.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241623 none CCOC1CC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 163, 163, 163, 90, 90, 90, 82, 82, 54, 54, 54, 42, 54, 30, 42, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 163, 163, 163, 163, 90, 82, 82, 82, 82, 54, 54, 54, 54, 54, 54, 54, 30, 30, 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: 685 number of broken/clashed sets: 105 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241623 none CCOC1CC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 1, 8, 8, 8, 9, 9, 15, 15, 15, 15, 34, 34, 48, 75, 163, 163, 163, 163, 163, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 48, 48, 163] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 30, 31] set([0, 1, 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: 394 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241623 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241623 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241623/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241623 Building REAL300025241624 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241624' /scratch/stefan/7787021/working/building/REAL300025241624 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241624 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241624/0 /scratch/stefan/7787021/working/building/REAL300025241624 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/499 `/scratch/stefan/7787021/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=NSN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241624.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241624 none CC(CCNC(=O)C1=NSN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', '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, 5, 8, 1, 11, 1, 8, 14, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 103, 119, 155, 157, 201, 201, 201, 201, 201, 201, 201, 63, 103, 27, 62, 13, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 155, 155, 157, 157, 201, 201, 103, 103, 103, 27, 27, 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: 792 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: REAL300025241624 none CC(CCNC(=O)C1=NSN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', '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, 5, 8, 1, 11, 1, 8, 14, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 17, 28, 28, 42, 42, 69, 108, 201, 201, 201, 201, 201, 17, 17, 17, 17, 10, 10, 8, 8, 2, 1, 28, 28, 28, 69, 69, 201] 201 rigid atoms, others: [33, 5, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 508 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241624 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241624 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241624/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241624 Building REAL300025241625 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241625' /scratch/stefan/7787021/working/building/REAL300025241625 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241625 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241625/0 /scratch/stefan/7787021/working/building/REAL300025241625 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/500 `/scratch/stefan/7787021/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CN=NS1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241625.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241625 none CC(CCNC(=O)C1=CN=NS1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', '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, 5, 8, 1, 11, 1, 1, 8, 8, 14, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 101, 123, 153, 158, 194, 194, 194, 201, 201, 201, 201, 68, 101, 29, 67, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 153, 153, 158, 158, 194, 201, 101, 101, 101, 29, 29, 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: 793 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: REAL300025241625 none CC(CCNC(=O)C1=CN=NS1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', '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, 5, 8, 1, 11, 1, 1, 8, 8, 14, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 12, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 17, 27, 27, 37, 37, 67, 104, 201, 201, 201, 201, 201, 17, 17, 17, 17, 12, 12, 10, 10, 4, 1, 27, 27, 27, 67, 67, 201] 201 rigid atoms, others: [33, 5, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 505 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241625 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241625 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241625/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241625 Building REAL300025241626 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241626' /scratch/stefan/7787021/working/building/REAL300025241626 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241626 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241626/0 /scratch/stefan/7787021/working/building/REAL300025241626 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/501 `/scratch/stefan/7787021/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241626.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241626 none COC(=O)NCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 6, 4, 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, 7] 0 hydrogens need 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, 74, 74, 74, 72, 72, 53, 52, 53, 40, 53, 30, 40, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 198, 198, 74, 72, 72, 72, 72, 53, 53, 53, 53, 53, 53, 53, 30, 30, 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: 840 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241626 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241626 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241626/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241626 Building REAL300025241627 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241627' /scratch/stefan/7787021/working/building/REAL300025241627 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241627 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241627/0 /scratch/stefan/7787021/working/building/REAL300025241627 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/502 `/scratch/stefan/7787021/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=NOC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241627.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241627 none CC(CCNC(=O)C1=NOC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 1, 8, 12, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 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] 0 hydrogens 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, 95, 111, 146, 167, 201, 201, 201, 201, 201, 201, 201, 58, 95, 27, 58, 13, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 146, 146, 167, 167, 201, 201, 201, 95, 95, 95, 27, 27, 1] 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]) total number of confs: 842 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: REAL300025241627 none CC(CCNC(=O)C1=NOC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 1, 8, 12, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 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] 0 hydrogens 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, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 16, 26, 26, 40, 40, 69, 108, 201, 201, 201, 201, 201, 16, 16, 16, 16, 9, 9, 7, 7, 2, 1, 1, 26, 26, 26, 69, 69, 201] 201 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 512 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241627 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241627 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241627/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241627 Building REAL300025241628 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241628' /scratch/stefan/7787021/working/building/REAL300025241628 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241628 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241628/0 /scratch/stefan/7787021/working/building/REAL300025241628 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/503 `/scratch/stefan/7787021/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCSCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241628.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241628 none CCCSCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 141, 138, 67, 67, 67, 67, 67, 46, 45, 46, 35, 46, 27, 35, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 138, 138, 67, 67, 67, 67, 67, 46, 46, 46, 46, 46, 46, 46, 27, 27, 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: 1019 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241628 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241628 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241628/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241628 Building REAL300025241629 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241629' /scratch/stefan/7787021/working/building/REAL300025241629 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241629 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241629/0 /scratch/stefan/7787021/working/building/REAL300025241629 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/504 `/scratch/stefan/7787021/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)C1CC1) `REAL300025241629.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241629 none CC(=CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)C1CC1 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.3', 'C.2', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 11, 11, 11, 21, 27, 35, 35, 35, 35, 39, 39, 74, 121, 201, 201, 201, 201, 201, 1, 1, 1, 3, 3, 3, 3, 11, 21, 21, 27, 27, 35, 35, 35, 35, 35, 35, 35, 74, 74, 201, 1, 1, 1, 1, 1] 201 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: 592 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241629 none CC(=CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)C1CC1 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.3', 'C.2', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 54, 54, 54, 54, 46, 41, 41, 41, 32, 41, 18, 32, 11, 1, 1, 1, 1, 1, 1, 1, 112, 201, 201, 112, 112, 112, 112, 54, 54, 54, 46, 46, 41, 41, 41, 41, 41, 41, 41, 18, 18, 1, 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]) total number of confs: 768 number of broken/clashed sets: 156 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241629 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241629 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241629/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241629 Building REAL300025241630 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241630' /scratch/stefan/7787021/working/building/REAL300025241630 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241630 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241630/0 /scratch/stefan/7787021/working/building/REAL300025241630 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/505 `/scratch/stefan/7787021/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1) `REAL300025241630.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241630 none CC1=NNC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 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, 7] 0 hydrogens need 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, 193, 193, 182, 162, 131, 110, 131, 82, 110, 32, 81, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 193, 182, 182, 162, 162, 131, 131, 131, 131, 110, 110, 110, 32, 32, 1, 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]) total number of confs: 797 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: REAL300025241630 none CC1=NNC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 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, 7] 0 hydrogens need rotated 201 conformations 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, 5, 11, 12, 18, 18, 25, 25, 36, 36, 71, 106, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 5, 11, 11, 14, 14, 18, 18, 18, 18, 25, 25, 25, 71, 71, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 24, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 534 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241630 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241630 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241630/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241630 Building REAL300025241631 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241631' /scratch/stefan/7787021/working/building/REAL300025241631 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241631 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241631/0 /scratch/stefan/7787021/working/building/REAL300025241631 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/506 `/scratch/stefan/7787021/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CN=CS1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241631.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241631 none CC(CCNC(=O)C1=CN=CS1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 1, 1, 8, 1, 14, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 103, 123, 156, 176, 194, 194, 194, 201, 201, 201, 201, 72, 103, 28, 72, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 156, 156, 176, 176, 194, 201, 201, 103, 103, 103, 28, 28, 1] 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]) total number of confs: 808 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: REAL300025241631 none CC(CCNC(=O)C1=CN=CS1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 1, 1, 8, 1, 14, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 13, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 19, 25, 25, 35, 35, 64, 103, 201, 201, 201, 201, 201, 19, 19, 19, 19, 14, 14, 11, 11, 5, 1, 1, 25, 25, 25, 64, 64, 201] 201 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 498 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241631 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241631 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241631/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241631 Building REAL300025241632 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241632' /scratch/stefan/7787021/working/building/REAL300025241632 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241632 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241632/0 /scratch/stefan/7787021/working/building/REAL300025241632 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/507 `/scratch/stefan/7787021/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1) `REAL300025241632.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241632 none CC1=NN(C)C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 118, 118, 118, 117, 108, 93, 79, 93, 58, 79, 26, 58, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 118, 117, 117, 108, 108, 93, 93, 93, 93, 79, 79, 79, 26, 26, 1, 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]) total number of confs: 631 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: REAL300025241632 none CC1=NN(C)C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 6, 6, 11, 12, 19, 19, 25, 25, 35, 35, 71, 111, 201, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 6, 11, 11, 13, 13, 19, 19, 19, 19, 25, 25, 25, 71, 71, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 47, 25] set([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, 44, 45, 46]) total number of confs: 543 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241632 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241632 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241632/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241632 Building REAL300025241633 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241633' /scratch/stefan/7787021/working/building/REAL300025241633 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241633 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241633/0 /scratch/stefan/7787021/working/building/REAL300025241633 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/508 `/scratch/stefan/7787021/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)N=C1) `REAL300025241633.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241633 none CC1=CN(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 97, 97, 97, 81, 81, 55, 50, 55, 37, 51, 26, 37, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 97, 81, 81, 81, 81, 55, 55, 55, 55, 51, 51, 51, 26, 26, 1, 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]) total number of confs: 881 number of broken/clashed sets: 83 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241633 none CC1=CN(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations 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, 9, 9, 9, 18, 18, 22, 22, 23, 23, 45, 45, 63, 101, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 5, 5, 9, 18, 18, 18, 18, 22, 22, 22, 22, 23, 23, 23, 63, 63, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 47, 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, 45, 46]) total number of confs: 523 number of broken/clashed sets: 83 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241633 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241633 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241633/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241633 Building REAL300025241634 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241634' /scratch/stefan/7787021/working/building/REAL300025241634 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241634 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241634/0 /scratch/stefan/7787021/working/building/REAL300025241634 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/509 `/scratch/stefan/7787021/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)COC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241634.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241634 none CC(C)COC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 192, 137, 192, 137, 137, 106, 106, 67, 62, 67, 45, 63, 30, 45, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 192, 192, 192, 192, 137, 106, 106, 106, 106, 67, 67, 67, 67, 63, 63, 63, 30, 30, 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: 969 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241634 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241634 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241634/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241634 Building REAL300025241635 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241635' /scratch/stefan/7787021/working/building/REAL300025241635 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241635 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241635/0 /scratch/stefan/7787021/working/building/REAL300025241635 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/510 `/scratch/stefan/7787021/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241635.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241635 none CCCC(=O)NCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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, 7, 6, 4, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 140, 140, 140, 104, 104, 104, 100, 100, 60, 59, 60, 42, 60, 29, 42, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 140, 140, 140, 104, 100, 100, 100, 100, 60, 60, 60, 60, 60, 60, 60, 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: 1000 number of broken/clashed sets: 98 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241635 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241635 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241635/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241635 Building REAL300025241636 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241636' /scratch/stefan/7787021/working/building/REAL300025241636 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241636 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241636/0 /scratch/stefan/7787021/working/building/REAL300025241636 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/511 `/scratch/stefan/7787021/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241636.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241636 none CCC=C(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 193, 102, 193, 102, 102, 102, 93, 79, 67, 79, 49, 67, 23, 48, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 193, 193, 193, 193, 102, 102, 102, 93, 93, 79, 79, 79, 79, 67, 67, 67, 23, 23, 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: 765 number of broken/clashed sets: 124 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241636 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241636 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241636/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241636 Building REAL300025241637 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241637' /scratch/stefan/7787021/working/building/REAL300025241637 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241637 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241637/0 /scratch/stefan/7787021/working/building/REAL300025241637 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/512 `/scratch/stefan/7787021/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CS(C)(=O)=O)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241637.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241637 none CC(CCNC(=O)CS(C)(=O)=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 14, 5, 11, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 6, 7, 7, 7, 7, 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: [88, 84, 88, 103, 134, 147, 147, 147, 201, 201, 201, 201, 70, 84, 30, 69, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 103, 103, 134, 134, 147, 201, 201, 201, 201, 201, 84, 84, 84, 30, 30, 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: 933 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241637 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241637 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241637/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241637 Building REAL300025241638 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241638' /scratch/stefan/7787021/working/building/REAL300025241638 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241638 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241638/0 /scratch/stefan/7787021/working/building/REAL300025241638 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/513 `/scratch/stefan/7787021/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C=C1CCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241638.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241638 none CC(CCNC(=O)C=C1CCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 100, 113, 129, 135, 137, 137, 137, 201, 201, 201, 201, 201, 201, 67, 100, 29, 67, 13, 1, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 129, 129, 135, 135, 137, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 100, 100, 100, 29, 29, 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: 761 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: REAL300025241638 none CC(CCNC(=O)C=C1CCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 17, 23, 23, 30, 30, 62, 100, 201, 201, 201, 201, 201, 17, 17, 17, 17, 14, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 62, 62, 201] 201 rigid atoms, others: [45, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 43, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 46, 47, 48, 49, 50, 51]) total number of confs: 505 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241638 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241638 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241638/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241638 Building REAL300025241639 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241639' /scratch/stefan/7787021/working/building/REAL300025241639 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241639 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241639/0 /scratch/stefan/7787021/working/building/REAL300025241639 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/514 `/scratch/stefan/7787021/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)N=CO1) `REAL300025241639.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241639 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 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 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, 182, 182, 160, 132, 102, 85, 102, 61, 85, 26, 60, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 182, 160, 160, 132, 132, 102, 102, 102, 102, 85, 85, 85, 26, 26, 1, 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]) total number of confs: 830 number of broken/clashed sets: 83 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241639 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 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 201 conformations 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, 14, 22, 22, 30, 30, 41, 41, 78, 122, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 3, 10, 10, 14, 14, 22, 22, 22, 22, 30, 30, 30, 78, 78, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 43, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 573 number of broken/clashed sets: 83 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241639 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241639 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241639/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241639 Building REAL300025241640 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241640' /scratch/stefan/7787021/working/building/REAL300025241640 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241640 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241640/0 /scratch/stefan/7787021/working/building/REAL300025241640 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/515 `/scratch/stefan/7787021/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(CC)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241640.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241640 none CCOC(CC)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 174, 201, 201, 174, 174, 170, 152, 125, 102, 125, 66, 102, 29, 65, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 174, 170, 170, 152, 152, 125, 125, 125, 125, 102, 102, 102, 29, 29, 1] 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]) total number of confs: 885 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241640 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241640 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241640/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241640 Building REAL300025241641 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241641' /scratch/stefan/7787021/working/building/REAL300025241641 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241641 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241641/0 /scratch/stefan/7787021/working/building/REAL300025241641 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/516 `/scratch/stefan/7787021/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC(F)(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241641.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241641 none CC(CCNC(=O)CC(F)(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 5, 5, 15, 15, 15, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 69, 82, 111, 113, 124, 124, 124, 201, 201, 201, 201, 48, 69, 25, 47, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 111, 111, 113, 113, 124, 201, 201, 69, 69, 69, 25, 25, 1] 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]) total number of confs: 899 number of broken/clashed sets: 118 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241641 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241641 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241641/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241641 Building REAL300025241642 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241642' /scratch/stefan/7787021/working/building/REAL300025241642 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241642 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241642/0 /scratch/stefan/7787021/working/building/REAL300025241642 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/517 `/scratch/stefan/7787021/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241642.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241642 none COC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 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, 7, 7] 0 hydrogens need 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, 197, 197, 188, 168, 136, 113, 136, 74, 113, 27, 73, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 197, 188, 188, 168, 168, 136, 136, 136, 136, 113, 113, 113, 27, 27, 1] 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]) total number of confs: 848 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241642 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241642 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241642/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241642 Building REAL300025241643 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241643' /scratch/stefan/7787021/working/building/REAL300025241643 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241643 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241643/0 /scratch/stefan/7787021/working/building/REAL300025241643 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/518 `/scratch/stefan/7787021/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241643.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241643 none CC(C)OCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 198, 123, 123, 123, 122, 109, 90, 72, 90, 50, 72, 29, 49, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 198, 198, 123, 122, 122, 109, 109, 90, 90, 90, 90, 72, 72, 72, 29, 29, 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: 972 number of broken/clashed sets: 123 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241643 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241643 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241643/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241643 Building REAL300025241644 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241644' /scratch/stefan/7787021/working/building/REAL300025241644 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241644 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241644/0 /scratch/stefan/7787021/working/building/REAL300025241644 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/519 `/scratch/stefan/7787021/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C(C)OCC1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241644.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241644 none CC(CCNC(=O)C(C)OCC1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 49, 49, 97, 97, 116, 148, 201, 201, 24, 35, 16, 24, 12, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 38, 38, 49, 97, 97, 97, 97, 148, 148, 201, 201, 201, 201, 201, 35, 35, 35, 16, 16, 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: 841 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241644 none CC(CCNC(=O)C(C)OCC1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 61, 46, 46, 32, 46, 22, 32, 9, 1, 1, 1, 1, 62, 62, 62, 79, 79, 116, 144, 201, 201, 201, 201, 201, 62, 62, 62, 62, 62, 62, 61, 61, 46, 32, 32, 32, 32, 9, 9, 1, 1, 1, 1, 1, 62, 62, 62, 116, 116, 201] 201 rigid atoms, others: [45, 43, 41, 42, 11, 12, 13, 44, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 49, 50, 51]) total number of confs: 639 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241644 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241644 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241644/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241644 Building REAL300025241645 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241645' /scratch/stefan/7787021/working/building/REAL300025241645 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241645 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241645/0 /scratch/stefan/7787021/working/building/REAL300025241645 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/520 `/scratch/stefan/7787021/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241645.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241645 none CCCOCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 192, 125, 125, 125, 107, 107, 69, 64, 69, 47, 65, 32, 47, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 192, 192, 125, 107, 107, 107, 107, 69, 69, 69, 69, 65, 65, 65, 32, 32, 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: 972 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241645 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241645 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241645/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241645 Building REAL300025241646 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241646' /scratch/stefan/7787021/working/building/REAL300025241646 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241646 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241646/0 /scratch/stefan/7787021/working/building/REAL300025241646 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/521 `/scratch/stefan/7787021/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241646.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241646 none CCCCOC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 90, 86, 86, 86, 86, 86, 74, 74, 49, 45, 49, 35, 46, 25, 35, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 100, 100, 86, 86, 86, 86, 86, 74, 74, 74, 74, 49, 49, 49, 49, 46, 46, 46, 25, 25, 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: 924 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241646 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241646 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241646/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241646 Building REAL300025241647 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241647' /scratch/stefan/7787021/working/building/REAL300025241647 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241647 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241647/0 /scratch/stefan/7787021/working/building/REAL300025241647 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/522 `/scratch/stefan/7787021/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCOC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241647.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241647 none C=CCCOC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 136, 126, 93, 72, 93, 72, 72, 58, 58, 42, 33, 42, 33, 33, 31, 33, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 136, 136, 93, 93, 93, 93, 72, 58, 58, 58, 58, 42, 42, 42, 42, 33, 33, 33, 31, 31, 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: 879 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241647 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241647 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241647/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241647 Building REAL300025241648 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241648' /scratch/stefan/7787021/working/building/REAL300025241648 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241648 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241648/0 /scratch/stefan/7787021/working/building/REAL300025241648 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/523 `/scratch/stefan/7787021/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCOC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241648.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241648 none CC(CCNC(=O)C1CCOC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 5, 12, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 89, 99, 117, 136, 146, 146, 146, 201, 201, 201, 201, 60, 89, 25, 60, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 99, 117, 117, 136, 136, 146, 201, 201, 201, 201, 201, 201, 201, 89, 89, 89, 25, 25, 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: 761 number of broken/clashed sets: 84 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241648 none CC(CCNC(=O)C1CCOC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 5, 12, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 8, 8, 1, 8, 1, 1, 1, 1, 1, 19, 24, 24, 32, 32, 66, 107, 201, 201, 201, 201, 201, 19, 19, 19, 19, 15, 15, 14, 14, 8, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 66, 66, 201] 201 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45]) total number of confs: 506 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241648 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241648 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241648/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241648 Building REAL300025241649 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241649' /scratch/stefan/7787021/working/building/REAL300025241649 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241649 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241649/0 /scratch/stefan/7787021/working/building/REAL300025241649 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/524 `/scratch/stefan/7787021/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=NC(F)=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241649.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241649 none CC(CCNC(=O)C1=CC=NC(F)=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 8, 1, 15, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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] 0 hydrogens 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, 65, 76, 77, 78, 78, 78, 78, 201, 201, 201, 201, 201, 201, 53, 65, 26, 53, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 77, 77, 78, 78, 78, 201, 201, 201, 65, 65, 65, 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: 457 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: REAL300025241649 none CC(CCNC(=O)C1=CC=NC(F)=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 8, 1, 15, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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] 0 hydrogens 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, 10, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 14, 19, 19, 23, 23, 46, 86, 201, 201, 201, 201, 201, 14, 14, 14, 14, 11, 11, 11, 11, 5, 1, 1, 1, 19, 19, 19, 46, 46, 201] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 448 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241649 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241649 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241649/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241649 Building REAL300025241650 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241650' /scratch/stefan/7787021/working/building/REAL300025241650 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241650 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241650/0 /scratch/stefan/7787021/working/building/REAL300025241650 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/525 `/scratch/stefan/7787021/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)S1) `REAL300025241650.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241650 none CC1=NC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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: [201, 201, 201, 201, 196, 196, 196, 183, 161, 127, 103, 127, 74, 103, 28, 73, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 196, 183, 183, 161, 161, 127, 127, 127, 127, 103, 103, 103, 28, 28, 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: 822 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241650 none CC1=NC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 1, 1, 4, 4, 4, 10, 13, 19, 19, 24, 24, 35, 35, 67, 106, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 4, 10, 10, 14, 14, 19, 19, 19, 19, 24, 24, 24, 67, 67, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 523 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241650 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241650 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241650/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241650 Building REAL300025241651 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241651' /scratch/stefan/7787021/working/building/REAL300025241651 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241651 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241651/0 /scratch/stefan/7787021/working/building/REAL300025241651 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/526 `/scratch/stefan/7787021/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=NN1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241651.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241651 none CC(CCNC(=O)C1=CC=NN1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [122, 103, 122, 150, 170, 184, 184, 184, 201, 201, 201, 201, 201, 72, 103, 30, 71, 13, 1, 1, 1, 1, 1, 1, 1, 122, 122, 122, 122, 150, 150, 170, 170, 184, 201, 201, 201, 201, 201, 103, 103, 103, 30, 30, 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: 792 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241651 none CC(CCNC(=O)C1=CC=NN1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [18, 12, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 18, 26, 26, 36, 36, 72, 107, 201, 201, 201, 201, 201, 18, 18, 18, 18, 13, 13, 11, 11, 4, 1, 1, 2, 2, 2, 26, 26, 26, 72, 72, 201] 201 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 532 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241651 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241651 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241651/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241651 Building REAL300025241652 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241652' /scratch/stefan/7787021/working/building/REAL300025241652 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241652 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241652/0 /scratch/stefan/7787021/working/building/REAL300025241652 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/527 `/scratch/stefan/7787021/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(OC)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241652.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241652 none CCC(OC)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 201, 168, 201, 201, 168, 168, 153, 129, 100, 82, 100, 57, 82, 24, 56, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 168, 153, 153, 129, 129, 100, 100, 100, 100, 82, 82, 82, 24, 24, 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: 929 number of broken/clashed sets: 107 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241652 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241652 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241652/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241652 Building REAL300025241653 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241653' /scratch/stefan/7787021/working/building/REAL300025241653 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241653 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241653/0 /scratch/stefan/7787021/working/building/REAL300025241653 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/528 `/scratch/stefan/7787021/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241653.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241653 none COCCCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 164, 161, 52, 52, 52, 52, 51, 46, 46, 46, 36, 46, 29, 36, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 164, 164, 164, 164, 161, 161, 52, 52, 52, 51, 51, 46, 46, 46, 46, 46, 46, 46, 29, 29, 1] 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]) total number of confs: 842 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241653 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241653 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241653/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241653 Building REAL300025241654 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241654' /scratch/stefan/7787021/working/building/REAL300025241654 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241654 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241654/0 /scratch/stefan/7787021/working/building/REAL300025241654 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/529 `/scratch/stefan/7787021/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241654.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241654 none CCCC(C)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 171, 201, 50, 50, 50, 50, 50, 49, 49, 49, 34, 49, 27, 34, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 171, 171, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 49, 27, 27, 1] 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]) total number of confs: 814 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241654 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241654 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241654/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241654 Building REAL300025241655 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241655' /scratch/stefan/7787021/working/building/REAL300025241655 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241655 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241655/0 /scratch/stefan/7787021/working/building/REAL300025241655 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/530 `/scratch/stefan/7787021/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241655.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241655 none COC(C)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 147, 147, 147, 137, 125, 99, 80, 99, 58, 80, 27, 57, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 147, 137, 137, 125, 125, 99, 99, 99, 99, 80, 80, 80, 27, 27, 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: 846 number of broken/clashed sets: 126 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241655 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241655 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241655/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241655 Building REAL300025241656 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241656' /scratch/stefan/7787021/working/building/REAL300025241656 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241656 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241656/0 /scratch/stefan/7787021/working/building/REAL300025241656 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/531 `/scratch/stefan/7787021/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1=CN(C)N=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241656.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241656 none CC(CCNC(=O)CC1=CN(C)N=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 1, 1, 8, 5, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [99, 88, 99, 110, 111, 122, 122, 122, 179, 201, 201, 201, 201, 201, 70, 88, 30, 69, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 99, 110, 110, 111, 111, 122, 179, 179, 201, 201, 201, 201, 201, 88, 88, 88, 30, 30, 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: 804 number of broken/clashed sets: 105 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241656 none CC(CCNC(=O)CC1=CN(C)N=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 1, 1, 8, 5, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [20, 16, 18, 12, 12, 5, 12, 1, 1, 1, 1, 1, 1, 1, 20, 22, 22, 26, 26, 58, 96, 201, 201, 201, 201, 201, 20, 20, 20, 20, 18, 18, 18, 18, 12, 5, 5, 1, 2, 2, 2, 1, 22, 22, 22, 58, 58, 201] 201 rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 13, 41] 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, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 506 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241656 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241656 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241656/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241656 Building REAL300025241657 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241657' /scratch/stefan/7787021/working/building/REAL300025241657 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241657 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241657/0 /scratch/stefan/7787021/working/building/REAL300025241657 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/532 `/scratch/stefan/7787021/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241657.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241657 none CC(CCNC(=O)C1CCCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [132, 115, 132, 153, 164, 164, 164, 164, 201, 201, 201, 201, 201, 201, 77, 115, 32, 77, 13, 1, 1, 1, 1, 1, 1, 1, 132, 132, 132, 132, 153, 153, 164, 164, 164, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 115, 115, 115, 32, 32, 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: 787 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: REAL300025241657 none CC(CCNC(=O)C1CCCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 13, 12, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 18, 22, 22, 29, 29, 59, 98, 201, 201, 201, 201, 201, 18, 18, 18, 18, 14, 14, 12, 12, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 59, 59, 201] 201 rigid atoms, others: [45, 35, 36, 5, 38, 7, 8, 9, 10, 39, 12, 13, 46, 44, 11, 40, 43, 41, 47, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 48, 49, 50, 51, 52, 53]) total number of confs: 495 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241657 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241657 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241657/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241657 Building REAL300025241658 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241658' /scratch/stefan/7787021/working/building/REAL300025241658 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241658 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241658/0 /scratch/stefan/7787021/working/building/REAL300025241658 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/533 `/scratch/stefan/7787021/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241658.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241658 none C=CCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 90, 90, 90, 90, 86, 69, 58, 69, 58, 58, 30, 57, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 90, 90, 90, 86, 86, 69, 69, 69, 69, 58, 58, 58, 30, 30, 1] 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]) total number of confs: 869 number of broken/clashed sets: 162 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241658 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241658 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241658/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241658 Building REAL300025241659 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241659' /scratch/stefan/7787021/working/building/REAL300025241659 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241659 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241659/0 /scratch/stefan/7787021/working/building/REAL300025241659 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/534 `/scratch/stefan/7787021/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=COCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241659.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241659 none CC(CCNC(=O)C1=COCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 100, 109, 117, 122, 122, 122, 122, 201, 201, 201, 201, 201, 75, 100, 30, 75, 13, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 109, 117, 117, 122, 122, 122, 201, 201, 201, 201, 201, 201, 201, 100, 100, 100, 30, 30, 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: 575 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241659 none CC(CCNC(=O)C1=COCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 19, 16, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 23, 27, 27, 33, 33, 71, 114, 201, 201, 201, 201, 201, 23, 23, 23, 23, 19, 19, 16, 16, 11, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 71, 71, 201] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46]) total number of confs: 532 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241659 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241659 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241659/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241659 Building REAL300025241660 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241660' /scratch/stefan/7787021/working/building/REAL300025241660 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241660 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241660/0 /scratch/stefan/7787021/working/building/REAL300025241660 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/535 `/scratch/stefan/7787021/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1CC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241660.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241660 none COC(=O)C1CC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 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, 7, 7] 0 hydrogens need 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, 138, 201, 138, 138, 60, 60, 60, 60, 60, 43, 43, 43, 33, 43, 25, 33, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 138, 138, 138, 138, 60, 60, 60, 60, 60, 43, 43, 43, 43, 43, 43, 43, 25, 25, 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: 692 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241660 none COC(=O)C1CC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 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, 7, 7] 0 hydrogens 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, 8, 8, 8, 14, 14, 15, 15, 15, 15, 33, 33, 48, 73, 138, 138, 138, 138, 138, 4, 4, 4, 1, 1, 1, 1, 8, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 48, 48, 138] 201 rigid atoms, others: [32, 2, 4, 5, 6, 7, 29, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 378 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241660 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241660 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241660/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241660 Building REAL300025241661 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241661' /scratch/stefan/7787021/working/building/REAL300025241661 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241661 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241661/0 /scratch/stefan/7787021/working/building/REAL300025241661 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/536 `/scratch/stefan/7787021/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCCOC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241661.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241661 none CC(CCNC(=O)C1CCCOC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 93, 105, 115, 120, 120, 120, 120, 201, 201, 201, 201, 201, 70, 93, 29, 70, 13, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 115, 115, 120, 120, 120, 201, 201, 201, 201, 201, 201, 201, 201, 201, 93, 93, 93, 29, 29, 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: 702 number of broken/clashed sets: 97 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241661 none CC(CCNC(=O)C1CCCOC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 23, 23, 30, 30, 67, 112, 201, 201, 201, 201, 201, 19, 19, 19, 19, 16, 16, 14, 14, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 67, 67, 201] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 523 number of broken/clashed sets: 97 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241661 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241661 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241661/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241661 Building REAL300025241662 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241662' /scratch/stefan/7787021/working/building/REAL300025241662 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241662 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241662/0 /scratch/stefan/7787021/working/building/REAL300025241662 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/537 `/scratch/stefan/7787021/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241662.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241662 none CCOCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens need 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, 122, 122, 122, 98, 98, 65, 54, 65, 44, 55, 28, 44, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 122, 98, 98, 98, 98, 65, 65, 65, 65, 55, 55, 55, 28, 28, 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: 928 number of broken/clashed sets: 109 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241662 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241662 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241662/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241662 Building REAL300025241663 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241663' /scratch/stefan/7787021/working/building/REAL300025241663 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241663 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241663/0 /scratch/stefan/7787021/working/building/REAL300025241663 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/538 `/scratch/stefan/7787021/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241663.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241663 none CCNC(=O)CCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 6] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 156, 156, 156, 156, 92, 92, 92, 79, 75, 64, 48, 64, 36, 49, 27, 36, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 156, 156, 156, 156, 156, 92, 79, 79, 75, 75, 64, 64, 64, 64, 49, 49, 49, 27, 27, 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: 969 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241663 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241663 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241663/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241663 Building REAL300025241664 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241664' /scratch/stefan/7787021/working/building/REAL300025241664 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241664 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241664/0 /scratch/stefan/7787021/working/building/REAL300025241664 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/539 `/scratch/stefan/7787021/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CSC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241664.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241664 none CC(CCNC(=O)C1=CSC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 1, 1, 14, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 104, 122, 158, 179, 201, 201, 201, 201, 201, 201, 201, 62, 104, 27, 62, 13, 1, 1, 1, 1, 1, 1, 1, 122, 122, 122, 122, 158, 158, 179, 179, 201, 201, 201, 104, 104, 104, 27, 27, 1] 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]) total number of confs: 835 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: REAL300025241664 none CC(CCNC(=O)C1=CSC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 1, 1, 14, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 24, 24, 37, 37, 68, 105, 201, 201, 201, 201, 201, 15, 15, 15, 15, 8, 8, 5, 5, 1, 1, 1, 24, 24, 24, 68, 68, 201] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 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]) total number of confs: 525 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241664 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241664 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241664/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241664 Building REAL300025241665 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241665' /scratch/stefan/7787021/working/building/REAL300025241665 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241665 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241665/0 /scratch/stefan/7787021/working/building/REAL300025241665 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/540 `/scratch/stefan/7787021/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241665.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241665 none COCC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 161, 201, 161, 161, 157, 133, 104, 97, 104, 69, 97, 30, 68, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 161, 157, 157, 133, 133, 104, 104, 104, 104, 97, 97, 97, 30, 30, 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: 867 number of broken/clashed sets: 137 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241665 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241665 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241665/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241665 Building REAL300025241666 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241666' /scratch/stefan/7787021/working/building/REAL300025241666 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241666 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241666/0 /scratch/stefan/7787021/working/building/REAL300025241666 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/541 `/scratch/stefan/7787021/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCCC(C)(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241666.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241666 none CC(CCNC(=O)CCCC(C)(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 53, 53, 53, 53, 148, 186, 201, 201, 186, 201, 45, 52, 26, 44, 13, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 53, 53, 53, 148, 148, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 52, 52, 52, 26, 26, 1] 201 rigid atoms, others: [55, 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, 51, 52, 53, 54]) total number of confs: 1074 number of broken/clashed sets: 123 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241666 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241666 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241666/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241666 Building REAL300025241667 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241667' /scratch/stefan/7787021/working/building/REAL300025241667 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241667 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241667/0 /scratch/stefan/7787021/working/building/REAL300025241667 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/542 `/scratch/stefan/7787021/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241667.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241667 none C=CCOCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 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, 7, 7] 0 hydrogens need 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, 175, 77, 77, 77, 61, 61, 55, 37, 55, 37, 37, 33, 37, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 175, 175, 77, 61, 61, 61, 61, 55, 55, 55, 55, 37, 37, 37, 33, 33, 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: 832 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241667 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241667 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241667/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241667 Building REAL300025241668 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241668' /scratch/stefan/7787021/working/building/REAL300025241668 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241668 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241668/0 /scratch/stefan/7787021/working/building/REAL300025241668 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/543 `/scratch/stefan/7787021/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=COC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241668.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241668 none CC(CCNC(=O)C1=COC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 1, 1, 12, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 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] 0 hydrogens 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, 105, 122, 158, 178, 201, 201, 201, 201, 201, 201, 201, 61, 105, 27, 61, 13, 1, 1, 1, 1, 1, 1, 1, 122, 122, 122, 122, 158, 158, 178, 178, 201, 201, 201, 105, 105, 105, 27, 27, 1] 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]) total number of confs: 832 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241668 none CC(CCNC(=O)C1=COC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 1, 1, 12, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 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] 0 hydrogens 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, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 23, 23, 36, 36, 66, 106, 201, 201, 201, 201, 201, 15, 15, 15, 15, 7, 7, 5, 5, 1, 1, 1, 23, 23, 23, 66, 66, 201] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 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]) total number of confs: 512 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241668 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241668 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241668/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241668 Building REAL300025241669 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241669' /scratch/stefan/7787021/working/building/REAL300025241669 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241669 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241669/0 /scratch/stefan/7787021/working/building/REAL300025241669 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/544 `/scratch/stefan/7787021/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)[C@H]1CCC(=O)N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241669.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241669 none CC(CCNC(=O)[C@H]1CCC(=O)N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 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: [107, 95, 107, 137, 163, 191, 191, 191, 201, 201, 201, 201, 201, 201, 62, 95, 26, 62, 13, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 137, 137, 163, 163, 191, 201, 201, 201, 201, 201, 95, 95, 95, 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: 837 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241669 none CC(CCNC(=O)[C@H]1CCC(=O)N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 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, 17, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 23, 30, 30, 41, 41, 77, 114, 201, 201, 201, 201, 201, 23, 23, 23, 23, 17, 17, 13, 13, 5, 1, 1, 1, 1, 1, 30, 30, 30, 77, 77, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45]) total number of confs: 550 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241669 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241669 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241669/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241669 Building REAL300025241670 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241670' /scratch/stefan/7787021/working/building/REAL300025241670 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241670 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241670/0 /scratch/stefan/7787021/working/building/REAL300025241670 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/545 `/scratch/stefan/7787021/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1=CCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241670.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241670 none CC(CCNC(=O)CC1=CCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 70, 77, 78, 78, 78, 199, 201, 201, 201, 201, 201, 56, 64, 25, 56, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 70, 70, 77, 77, 78, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 201, 64, 64, 64, 25, 25, 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: 825 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: REAL300025241670 none CC(CCNC(=O)CC1=CCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 25, 21, 17, 17, 5, 17, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 33, 33, 68, 109, 201, 201, 201, 201, 201, 30, 30, 30, 30, 25, 25, 21, 21, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 68, 68, 201] 201 rigid atoms, others: [45, 43, 37, 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, 46, 47, 48, 49, 50, 51]) total number of confs: 521 number of broken/clashed sets: 109 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241670 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241670 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241670/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241670 Building REAL300025241671 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241671' /scratch/stefan/7787021/working/building/REAL300025241671 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241671 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241671/0 /scratch/stefan/7787021/working/building/REAL300025241671 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/546 `/scratch/stefan/7787021/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)N1) `REAL300025241671.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241671 none CC1=NC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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 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, 192, 192, 192, 173, 154, 126, 108, 126, 75, 108, 29, 75, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 192, 173, 173, 154, 154, 126, 126, 126, 126, 108, 108, 108, 29, 29, 1, 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]) total number of confs: 784 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: REAL300025241671 none CC1=NC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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 201 conformations 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, 5, 12, 15, 20, 20, 27, 27, 34, 34, 67, 107, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 5, 12, 12, 15, 15, 20, 20, 20, 20, 27, 27, 27, 67, 67, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 24, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 515 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241671 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241671 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241671/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241671 Building REAL300025241672 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241672' /scratch/stefan/7787021/working/building/REAL300025241672 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241672 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241672/0 /scratch/stefan/7787021/working/building/REAL300025241672 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/547 `/scratch/stefan/7787021/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241672.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241672 none CSCC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 163, 163, 120, 163, 120, 120, 118, 99, 86, 84, 86, 63, 84, 26, 62, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 163, 163, 163, 163, 163, 163, 120, 118, 118, 99, 99, 86, 86, 86, 86, 84, 84, 84, 26, 26, 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: 751 number of broken/clashed sets: 140 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241672 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241672 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241672/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241672 Building REAL300025241673 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241673' /scratch/stefan/7787021/working/building/REAL300025241673 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241673 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241673/0 /scratch/stefan/7787021/working/building/REAL300025241673 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/548 `/scratch/stefan/7787021/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCC[N@@H+]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241673.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241673 none CC(CCNC(=O)C1CCC[N@@H+]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 133, 150, 183, 183, 201, 201, 201, 201, 201, 201, 201, 201, 201, 105, 133, 35, 105, 13, 1, 1, 1, 1, 1, 1, 1, 150, 150, 150, 150, 183, 183, 183, 183, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 133, 133, 133, 35, 35, 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: 784 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241673 none CC(CCNC(=O)C1CCC[N@@H+]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 16, 22, 22, 29, 29, 73, 118, 201, 201, 201, 201, 201, 16, 16, 16, 16, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 22, 22, 22, 73, 73, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 554 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241673 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241673/1 /scratch/stefan/7787021/working/building/REAL300025241673 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/549 `/scratch/stefan/7787021/working/3D/549' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCC[N@H+]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241673.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241673/1/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: REAL300025241673 none CC(CCNC(=O)C1CCC[N@H+]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 137, 152, 185, 185, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 137, 34, 106, 13, 1, 1, 1, 1, 1, 1, 1, 152, 152, 152, 152, 185, 185, 185, 185, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 137, 137, 137, 34, 34, 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: 775 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241673 none CC(CCNC(=O)C1CCC[N@H+]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 16, 22, 22, 29, 29, 73, 116, 201, 201, 201, 201, 201, 16, 16, 16, 16, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 22, 22, 22, 73, 73, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 555 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241673 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241673 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241673/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241673/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241673 Building REAL300025241674 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241674' /scratch/stefan/7787021/working/building/REAL300025241674 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241674 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241674/0 /scratch/stefan/7787021/working/building/REAL300025241674 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/550 `/scratch/stefan/7787021/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241674.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241674 none CCC(=O)NCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 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, 6, 4, 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, 7, 7, 7] 0 hydrogens need 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, 88, 88, 88, 83, 83, 59, 59, 59, 44, 59, 32, 44, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 130, 130, 130, 88, 83, 83, 83, 83, 59, 59, 59, 59, 59, 59, 59, 32, 32, 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: 1021 number of broken/clashed sets: 102 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241674 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241674 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241674/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241674 Building REAL300025241675 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241675' /scratch/stefan/7787021/working/building/REAL300025241675 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241675 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241675/0 /scratch/stefan/7787021/working/building/REAL300025241675 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/551 `/scratch/stefan/7787021/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C=CC(C)(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241675.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241675 none CC(CCNC(=O)C=CC(C)(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 70, 76, 85, 90, 91, 91, 91, 201, 201, 201, 201, 201, 56, 70, 25, 55, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 85, 85, 90, 90, 91, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 70, 70, 70, 25, 25, 1] 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]) total number of confs: 683 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241675 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241675 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241675/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241675 Building REAL300025241676 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241676' /scratch/stefan/7787021/working/building/REAL300025241676 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241676 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241676/0 /scratch/stefan/7787021/working/building/REAL300025241676 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/552 `/scratch/stefan/7787021/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=C(F)N=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241676.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241676 none CC(CCNC(=O)C1=CC=C(F)N=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 1, 15, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 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: [139, 119, 139, 156, 161, 167, 167, 167, 201, 201, 201, 201, 201, 201, 89, 119, 32, 89, 13, 1, 1, 1, 1, 1, 1, 1, 139, 139, 139, 139, 156, 156, 161, 161, 167, 201, 201, 201, 119, 119, 119, 32, 32, 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: 697 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: REAL300025241676 none CC(CCNC(=O)C1=CC=C(F)N=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 1, 15, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 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: [18, 13, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 18, 24, 24, 30, 30, 70, 118, 201, 201, 201, 201, 201, 18, 18, 18, 18, 15, 15, 14, 14, 5, 1, 1, 1, 24, 24, 24, 70, 70, 201] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 527 number of broken/clashed sets: 109 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241676 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241676 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241676/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241676 Building REAL300025241677 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241677' /scratch/stefan/7787021/working/building/REAL300025241677 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241677 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241677/0 /scratch/stefan/7787021/working/building/REAL300025241677 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/553 `/scratch/stefan/7787021/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241677.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241677 none COCCOCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens need 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, 151, 62, 62, 62, 48, 48, 40, 30, 40, 30, 30, 28, 30, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 151, 151, 62, 48, 48, 48, 48, 40, 40, 40, 40, 30, 30, 30, 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: 718 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241677 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241677 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241677/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241677 Building REAL300025241678 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241678' /scratch/stefan/7787021/working/building/REAL300025241678 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241678 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241678/0 /scratch/stefan/7787021/working/building/REAL300025241678 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/554 `/scratch/stefan/7787021/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241678.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241678 none CCCC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 124, 188, 124, 124, 114, 106, 95, 89, 95, 68, 89, 32, 67, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 188, 188, 188, 188, 124, 114, 114, 106, 106, 95, 95, 95, 95, 89, 89, 89, 32, 32, 1] 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]) total number of confs: 867 number of broken/clashed sets: 142 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241678 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241678 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241678/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241678 Building REAL300025241679 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241679' /scratch/stefan/7787021/working/building/REAL300025241679 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241679 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241679/0 /scratch/stefan/7787021/working/building/REAL300025241679 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/555 `/scratch/stefan/7787021/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241679.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241679 none CC1=NN(C)C=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 185, 185, 185, 181, 169, 140, 115, 140, 84, 115, 30, 84, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 185, 181, 181, 169, 169, 140, 140, 140, 140, 115, 115, 115, 30, 30, 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: 785 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: REAL300025241679 none CC1=NN(C)C=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 201 conformations 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, 3, 3, 4, 12, 13, 18, 18, 25, 25, 32, 32, 74, 107, 201, 201, 201, 201, 201, 2, 2, 2, 2, 2, 2, 1, 4, 12, 12, 14, 14, 18, 18, 18, 18, 25, 25, 25, 74, 74, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 548 number of broken/clashed sets: 109 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241679 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241679 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241679/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241679 Building REAL300025241680 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241680' /scratch/stefan/7787021/working/building/REAL300025241680 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241680 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241680/0 /scratch/stefan/7787021/working/building/REAL300025241680 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/556 `/scratch/stefan/7787021/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CC2CCC1O2)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241680.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241680 none CC(CCNC(=O)C1CC2CCC1O2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 99, 112, 152, 173, 193, 193, 193, 201, 201, 201, 201, 201, 201, 62, 99, 28, 62, 13, 1, 1, 1, 1, 1, 1, 1, 112, 112, 112, 112, 152, 152, 173, 173, 193, 201, 201, 201, 201, 201, 201, 201, 201, 201, 99, 99, 99, 28, 28, 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: 849 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241680 none CC(CCNC(=O)C1CC2CCC1O2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 18, 26, 26, 36, 36, 67, 106, 201, 201, 201, 201, 201, 18, 18, 18, 18, 12, 12, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 67, 67, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 40, 43, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 510 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241680 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241680 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241680/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241680 Building REAL300025241681 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241681' /scratch/stefan/7787021/working/building/REAL300025241681 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241681 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241681/0 /scratch/stefan/7787021/working/building/REAL300025241681 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/557 `/scratch/stefan/7787021/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=NO1) `REAL300025241681.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241681 none CC1=CC(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 78, 78, 76, 76, 53, 47, 53, 34, 48, 25, 34, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 78, 76, 76, 76, 76, 53, 53, 53, 53, 48, 48, 48, 25, 25, 1] 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]) total number of confs: 863 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: REAL300025241681 none CC1=CC(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 9, 9, 9, 15, 15, 20, 20, 20, 20, 43, 43, 58, 99, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 3, 3, 9, 15, 15, 15, 15, 20, 20, 20, 20, 20, 20, 20, 58, 58, 201] 201 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, 45, 46]) total number of confs: 515 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241681 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241681 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241681/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241681 Building REAL300025241682 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241682' /scratch/stefan/7787021/working/building/REAL300025241682 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241682 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241682/0 /scratch/stefan/7787021/working/building/REAL300025241682 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/558 `/scratch/stefan/7787021/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=N1) `REAL300025241682.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241682 none CCN1C=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 85, 85, 85, 85, 85, 56, 56, 56, 40, 56, 28, 40, 13, 1, 1, 1, 1, 1, 1, 1, 151, 151, 201, 201, 201, 201, 201, 151, 85, 85, 85, 85, 85, 56, 56, 56, 56, 56, 56, 56, 28, 28, 1, 151] 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]) total number of confs: 783 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: REAL300025241682 none CCN1C=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 8, 9, 9, 9, 9, 21, 21, 31, 51, 151, 151, 151, 151, 151, 1, 1, 6, 6, 6, 6, 6, 1, 5, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 31, 31, 151, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 47, 24, 25, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 325 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241682 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241682 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241682/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241682 Building REAL300025241683 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241683' /scratch/stefan/7787021/working/building/REAL300025241683 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241683 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241683/0 /scratch/stefan/7787021/working/building/REAL300025241683 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/559 `/scratch/stefan/7787021/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=NC=CN=C1N)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241683.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241683 none CC(CCNC(=O)C1=NC=CN=C1N)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 6, 7, 7, 7, 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: [120, 100, 120, 157, 180, 200, 200, 200, 201, 201, 201, 201, 201, 201, 65, 100, 27, 65, 13, 1, 1, 1, 1, 1, 1, 1, 120, 120, 120, 120, 157, 157, 180, 180, 200, 201, 201, 201, 201, 100, 100, 100, 27, 27, 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: 846 number of broken/clashed sets: 66 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241683 none CC(CCNC(=O)C1=NC=CN=C1N)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 6, 7, 7, 7, 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: [20, 12, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 20, 30, 30, 39, 39, 70, 108, 201, 201, 201, 201, 201, 20, 20, 20, 20, 13, 13, 9, 9, 4, 1, 1, 2, 2, 30, 30, 30, 70, 70, 201] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 532 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241683 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241683 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241683/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241683 Building REAL300025241684 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241684' /scratch/stefan/7787021/working/building/REAL300025241684 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241684 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241684/0 /scratch/stefan/7787021/working/building/REAL300025241684 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/560 `/scratch/stefan/7787021/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241684.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241684 none CC(CCNC(=O)CCC1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 49, 56, 56, 56, 56, 56, 153, 160, 201, 201, 48, 48, 26, 48, 13, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 56, 56, 56, 56, 56, 153, 153, 160, 160, 201, 201, 201, 201, 201, 48, 48, 48, 26, 26, 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: 813 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: REAL300025241684 none CC(CCNC(=O)CCC1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 5, 21, 3, 1, 1, 1, 1, 36, 37, 37, 37, 37, 72, 115, 201, 201, 201, 201, 201, 36, 36, 36, 36, 36, 36, 29, 29, 21, 5, 5, 3, 3, 1, 1, 1, 1, 1, 37, 37, 37, 72, 72, 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]) total number of confs: 562 number of broken/clashed sets: 146 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241684 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241684 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241684/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241684 Building REAL300025241685 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241685' /scratch/stefan/7787021/working/building/REAL300025241685 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241685 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241685/0 /scratch/stefan/7787021/working/building/REAL300025241685 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/561 `/scratch/stefan/7787021/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=NN1) `REAL300025241685.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241685 none CC1=C(C)C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 201, 196, 196, 196, 176, 149, 114, 96, 114, 67, 96, 27, 66, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 196, 176, 176, 149, 149, 114, 114, 114, 114, 96, 96, 96, 27, 27, 1, 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]) total number of confs: 850 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: REAL300025241685 none CC1=C(C)C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 1, 3, 3, 3, 11, 13, 22, 22, 36, 36, 44, 44, 72, 107, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 2, 2, 2, 3, 11, 11, 15, 15, 22, 22, 22, 22, 36, 36, 36, 72, 72, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 24, 25] set([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]) total number of confs: 558 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241685 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241685/1 /scratch/stefan/7787021/working/building/REAL300025241685 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/562 `/scratch/stefan/7787021/working/3D/562' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1C) `REAL300025241685.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241685/1/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: REAL300025241685 none CC1=NNC(C(=O)NCCC(C)N(C)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', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7] 0 hydrogens need 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, 91, 87, 82, 75, 82, 61, 75, 26, 60, 11, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 91, 91, 91, 87, 87, 82, 82, 82, 82, 75, 75, 75, 26, 26, 1, 201, 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]) total number of confs: 512 number of broken/clashed sets: 97 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241685 none CC1=NNC(C(=O)NCCC(C)N(C)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', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 9, 9, 9, 15, 18, 25, 25, 27, 27, 32, 32, 64, 112, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 9, 15, 15, 19, 19, 25, 25, 25, 25, 27, 27, 27, 64, 64, 201, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 29] set([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, 45, 46, 47]) total number of confs: 534 number of broken/clashed sets: 97 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241685 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241685 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241685/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241685/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241685 Building REAL300025241686 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241686' /scratch/stefan/7787021/working/building/REAL300025241686 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241686 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241686/0 /scratch/stefan/7787021/working/building/REAL300025241686 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/563 `/scratch/stefan/7787021/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1CCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241686.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241686 none CC(CCNC(=O)CC1CCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 62, 62, 62, 62, 171, 201, 201, 201, 201, 201, 51, 59, 24, 50, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 62, 62, 62, 171, 171, 201, 201, 201, 201, 201, 201, 201, 201, 201, 59, 59, 59, 24, 24, 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: 784 number of broken/clashed sets: 135 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241686 none CC(CCNC(=O)CC1CCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 26, 23, 23, 5, 23, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 30, 30, 65, 104, 201, 201, 201, 201, 201, 27, 27, 27, 27, 27, 27, 26, 26, 23, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 65, 65, 201] 201 rigid atoms, others: [45, 11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 44, 40, 43, 41, 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, 46, 47, 48, 49, 50, 51]) total number of confs: 500 number of broken/clashed sets: 135 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241686 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241686 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241686/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241686 Building REAL300025241687 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241687' /scratch/stefan/7787021/working/building/REAL300025241687 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241687 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241687/0 /scratch/stefan/7787021/working/building/REAL300025241687 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/564 `/scratch/stefan/7787021/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241687.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241687 none CCCCOCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 124, 116, 107, 53, 53, 53, 46, 46, 41, 33, 41, 33, 33, 31, 33, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 124, 124, 107, 107, 53, 46, 46, 46, 46, 41, 41, 41, 41, 33, 33, 33, 31, 31, 1] 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]) total number of confs: 896 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241687 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241687 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241687/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241687 Building REAL300025241688 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241688' /scratch/stefan/7787021/working/building/REAL300025241688 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241688 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241688/0 /scratch/stefan/7787021/working/building/REAL300025241688 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/565 `/scratch/stefan/7787021/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1=NOC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241688.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241688 none CC(CCNC(=O)CC1=NOC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 5, 1, 8, 12, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 101, 126, 129, 129, 129, 201, 201, 201, 201, 201, 60, 88, 29, 60, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 101, 101, 126, 126, 129, 201, 201, 201, 201, 88, 88, 88, 29, 29, 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: 909 number of broken/clashed sets: 122 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241688 none CC(CCNC(=O)CC1=NOC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 5, 1, 8, 12, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 21, 16, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 27, 27, 27, 36, 36, 73, 107, 201, 201, 201, 201, 201, 27, 27, 27, 27, 21, 21, 16, 16, 9, 3, 3, 1, 1, 27, 27, 27, 73, 73, 201] 201 rigid atoms, others: [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, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 560 number of broken/clashed sets: 122 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241688 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241688 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241688/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241688 Building REAL300025241689 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241689' /scratch/stefan/7787021/working/building/REAL300025241689 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241689 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241689/0 /scratch/stefan/7787021/working/building/REAL300025241689 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/566 `/scratch/stefan/7787021/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)N=CO1) `REAL300025241689.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241689 none CCC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 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, 190, 190, 190, 190, 190, 177, 153, 116, 93, 116, 55, 93, 25, 55, 13, 1, 1, 1, 1, 1, 1, 1, 190, 190, 190, 201, 201, 201, 201, 201, 190, 177, 177, 153, 153, 116, 116, 116, 116, 93, 93, 93, 25, 25, 1, 190] 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]) total number of confs: 890 number of broken/clashed sets: 98 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241689 none CCC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 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: [3, 1, 1, 1, 1, 1, 1, 1, 6, 7, 13, 13, 18, 18, 27, 27, 57, 91, 190, 190, 190, 190, 190, 1, 1, 1, 4, 4, 4, 3, 3, 1, 6, 6, 7, 7, 13, 13, 13, 13, 18, 18, 18, 57, 57, 190, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 46, 23, 24, 25, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 486 number of broken/clashed sets: 98 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241689 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241689 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241689/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241689 Building REAL300025241690 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241690' /scratch/stefan/7787021/working/building/REAL300025241690 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241690 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241690/0 /scratch/stefan/7787021/working/building/REAL300025241690 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/567 `/scratch/stefan/7787021/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1CCOC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241690.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241690 none CC(CCNC(=O)CC1CCOC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 88, 88, 88, 88, 184, 201, 201, 201, 201, 73, 83, 28, 72, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 83, 88, 88, 88, 184, 184, 201, 201, 201, 201, 201, 201, 201, 83, 83, 83, 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: 785 number of broken/clashed sets: 118 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241690 none CC(CCNC(=O)CC1CCOC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 21, 21, 5, 21, 1, 1, 1, 1, 1, 1, 28, 28, 28, 31, 31, 77, 120, 201, 201, 201, 201, 201, 28, 28, 28, 28, 28, 28, 24, 24, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 77, 77, 201] 201 rigid atoms, others: [36, 37, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 530 number of broken/clashed sets: 118 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241690 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241690 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241690/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241690 Building REAL300025241691 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241691' /scratch/stefan/7787021/working/building/REAL300025241691 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241691 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241691/0 /scratch/stefan/7787021/working/building/REAL300025241691 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/568 `/scratch/stefan/7787021/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CC=CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241691.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241691 none CC(CCNC(=O)C1CC=CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 1, 1, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7] 0 hydrogens 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, 79, 85, 89, 93, 94, 94, 94, 201, 201, 201, 201, 64, 79, 25, 64, 12, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 89, 89, 93, 93, 94, 201, 201, 201, 201, 201, 201, 201, 79, 79, 79, 25, 25, 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: 676 number of broken/clashed sets: 98 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241691 none CC(CCNC(=O)C1CC=CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 1, 1, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7] 0 hydrogens 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, 14, 9, 9, 1, 9, 1, 1, 1, 1, 1, 22, 24, 24, 29, 29, 65, 103, 201, 201, 201, 201, 201, 22, 22, 22, 22, 17, 17, 14, 14, 9, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 65, 65, 201] 201 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45]) total number of confs: 520 number of broken/clashed sets: 98 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241691 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241691 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241691/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241691 Building REAL300025241692 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241692' /scratch/stefan/7787021/working/building/REAL300025241692 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241692 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241692/0 /scratch/stefan/7787021/working/building/REAL300025241692 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/569 `/scratch/stefan/7787021/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1=NNC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241692.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241692 none CC(CCNC(=O)CC1=NNC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 1, 8, 8, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 51, 60, 79, 104, 112, 112, 112, 201, 201, 201, 201, 201, 51, 51, 29, 51, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 79, 79, 104, 104, 112, 201, 201, 201, 201, 201, 51, 51, 51, 29, 29, 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: 916 number of broken/clashed sets: 141 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241692 none CC(CCNC(=O)CC1=NNC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 1, 8, 8, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 22, 11, 11, 5, 11, 1, 1, 1, 1, 1, 1, 37, 38, 38, 40, 40, 78, 107, 201, 201, 201, 201, 201, 37, 37, 37, 37, 28, 28, 22, 22, 11, 5, 5, 1, 1, 1, 38, 38, 38, 78, 78, 201] 201 rigid atoms, others: [36, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 601 number of broken/clashed sets: 141 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241692 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241692 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241692/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241692 Building REAL300025241693 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241693' /scratch/stefan/7787021/working/building/REAL300025241693 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241693 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241693/0 /scratch/stefan/7787021/working/building/REAL300025241693 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/570 `/scratch/stefan/7787021/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=NC=C1F)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241693.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241693 none CC(CCNC(=O)C1=CC=NC=C1F)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 15, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 105, 125, 152, 171, 183, 183, 183, 201, 201, 201, 201, 201, 201, 72, 105, 27, 72, 13, 1, 1, 1, 1, 1, 1, 1, 125, 125, 125, 125, 152, 152, 171, 171, 183, 201, 201, 201, 105, 105, 105, 27, 27, 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: 778 number of broken/clashed sets: 74 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241693 none CC(CCNC(=O)C1=CC=NC=C1F)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 15, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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] 0 hydrogens 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, 13, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 19, 27, 27, 36, 36, 74, 114, 201, 201, 201, 201, 201, 19, 19, 19, 19, 14, 14, 12, 12, 4, 1, 1, 1, 27, 27, 27, 74, 74, 201] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 546 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241693 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241693 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241693/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241693 Building REAL300025241694 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241694' /scratch/stefan/7787021/working/building/REAL300025241694 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241694 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241694/0 /scratch/stefan/7787021/working/building/REAL300025241694 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/571 `/scratch/stefan/7787021/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)N=NN1C) `REAL300025241694.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241694 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 156, 156, 140, 124, 96, 80, 96, 48, 80, 23, 48, 11, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 156, 140, 140, 124, 124, 96, 96, 96, 96, 80, 80, 80, 23, 23, 1, 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]) total number of confs: 757 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241694 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 4, 10, 14, 21, 21, 30, 30, 45, 45, 83, 122, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 4, 10, 10, 14, 14, 21, 21, 21, 21, 30, 30, 30, 83, 83, 201, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24, 25] set([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, 45, 46]) total number of confs: 594 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241694 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241694 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241694/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241694 Building REAL300025241695 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241695' /scratch/stefan/7787021/working/building/REAL300025241695 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241695 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241695/0 /scratch/stefan/7787021/working/building/REAL300025241695 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/572 `/scratch/stefan/7787021/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241695.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241695 none CC1=CC=NC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 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, 7] 0 hydrogens need 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, 91, 91, 91, 90, 85, 78, 73, 78, 56, 73, 22, 56, 11, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 91, 90, 90, 85, 85, 78, 78, 78, 78, 73, 73, 73, 22, 22, 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: 507 number of broken/clashed sets: 114 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241695 none CC1=CC=NC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 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, 7] 0 hydrogens need rotated 201 conformations 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, 14, 18, 24, 24, 26, 26, 34, 34, 74, 114, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 9, 14, 14, 18, 18, 24, 24, 24, 24, 26, 26, 26, 74, 74, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 555 number of broken/clashed sets: 114 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241695 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241695 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241695/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241695 Building REAL300025241696 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241696' /scratch/stefan/7787021/working/building/REAL300025241696 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241696 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241696/0 /scratch/stefan/7787021/working/building/REAL300025241696 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/573 `/scratch/stefan/7787021/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1) `REAL300025241696.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241696 none CC1=CN=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 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, 7, 7] 0 hydrogens need 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, 97, 97, 97, 97, 94, 90, 74, 90, 58, 74, 28, 57, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 97, 97, 97, 94, 94, 90, 90, 90, 90, 74, 74, 74, 28, 28, 1, 201] 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]) total number of confs: 540 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241696 none CC1=CN=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 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, 7, 7] 0 hydrogens need rotated 201 conformations 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, 11, 11, 16, 16, 21, 21, 25, 25, 54, 92, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 5, 11, 11, 12, 12, 16, 16, 16, 16, 21, 21, 21, 54, 54, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 46, 25, 29, 30] set([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: 490 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241696 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241696 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241696/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241696 Building REAL300025241697 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241697' /scratch/stefan/7787021/working/building/REAL300025241697 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300025241697 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241697/0 /scratch/stefan/7787021/working/building/REAL300025241697 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/574 `/scratch/stefan/7787021/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CN(C)CCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241697.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241697 none CC(CCNC(=O)C1CN(C)CCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 10, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 84, 103, 132, 156, 165, 165, 165, 201, 201, 201, 201, 201, 201, 56, 84, 26, 56, 11, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 132, 132, 156, 156, 165, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 84, 84, 84, 26, 26, 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: 871 number of broken/clashed sets: 101 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241697 none CC(CCNC(=O)C1CN(C)CCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 10, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 26, 32, 32, 43, 43, 80, 120, 201, 201, 201, 201, 201, 26, 26, 26, 26, 20, 20, 14, 14, 6, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 32, 32, 32, 80, 80, 201] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 44, 43, 41, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 45, 46, 47, 48, 49, 50]) total number of confs: 596 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241697 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241697/1 /scratch/stefan/7787021/working/building/REAL300025241697 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/575 `/scratch/stefan/7787021/working/3D/575' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1C[N@H+](C)CCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241697.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241697/1/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: REAL300025241697 none CC(CCNC(=O)C1C[N@H+](C)CCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 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: [99, 89, 99, 116, 116, 119, 119, 119, 124, 124, 124, 124, 124, 124, 124, 79, 89, 32, 79, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 99, 116, 116, 116, 116, 119, 124, 124, 124, 124, 124, 124, 124, 124, 124, 124, 89, 89, 89, 32, 32, 1] 124 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: 475 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: REAL300025241697 none CC(CCNC(=O)C1C[N@H+](C)CCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 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: [13, 8, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 13, 17, 17, 21, 21, 53, 74, 124, 124, 124, 124, 124, 13, 13, 13, 13, 13, 13, 13, 13, 4, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 17, 17, 17, 53, 53, 124] 124 rigid atoms, others: [45, 43, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 44, 42, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 46, 47, 48, 49, 50, 51]) total number of confs: 382 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241697 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `2' /scratch/stefan/7787021/working/building/REAL300025241697/2 /scratch/stefan/7787021/working/building/REAL300025241697 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 2 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/576 `/scratch/stefan/7787021/working/3D/576' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1C[N@@H+](C)CCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241697.mol2' -> `2.mol2' `temp.mol2' -> `REAL300025241697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241697/2/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: REAL300025241697 none CC(CCNC(=O)C1C[N@@H+](C)CCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 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: [86, 73, 86, 99, 101, 103, 103, 103, 103, 103, 103, 103, 103, 103, 103, 72, 73, 32, 72, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 99, 99, 101, 101, 103, 103, 103, 103, 103, 103, 103, 103, 103, 103, 103, 73, 73, 73, 32, 32, 1] 103 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: 405 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: REAL300025241697 none CC(CCNC(=O)C1C[N@@H+](C)CCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 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: [13, 10, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 13, 16, 16, 17, 17, 35, 53, 103, 103, 103, 103, 103, 13, 13, 13, 13, 12, 12, 12, 12, 4, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 16, 16, 16, 35, 35, 103] 103 rigid atoms, others: [45, 43, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 44, 42, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 46, 47, 48, 49, 50, 51]) total number of confs: 275 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241697 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241697 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241697/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241697/1.* 2: /scratch/stefan/7787021/working/building/REAL300025241697/2.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241697 Building REAL300025241698 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241698' /scratch/stefan/7787021/working/building/REAL300025241698 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241698 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241698/0 /scratch/stefan/7787021/working/building/REAL300025241698 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/577 `/scratch/stefan/7787021/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C)=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)O1) `REAL300025241698.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241698 none CC1=NC(C)=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 163, 163, 163, 154, 139, 115, 98, 115, 70, 98, 28, 69, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 163, 154, 154, 139, 139, 115, 115, 115, 115, 98, 98, 98, 28, 28, 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: 722 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241698 none CC1=NC(C)=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 14, 24, 24, 30, 30, 40, 40, 80, 125, 201, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 3, 9, 9, 14, 14, 24, 24, 24, 24, 30, 30, 30, 80, 80, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25] set([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, 44, 45, 46]) total number of confs: 581 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241698 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241698 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241698/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241698 Building REAL300025241699 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241699' /scratch/stefan/7787021/working/building/REAL300025241699 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241699 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241699/0 /scratch/stefan/7787021/working/building/REAL300025241699 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/578 `/scratch/stefan/7787021/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC(F)(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241699.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241699 none CC(CCNC(=O)CCC(F)(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 5, 5, 5, 15, 15, 15, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 91, 96, 96, 101, 102, 102, 102, 197, 201, 201, 201, 201, 70, 91, 28, 69, 13, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 96, 96, 101, 101, 102, 197, 197, 201, 201, 91, 91, 91, 28, 28, 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: 821 number of broken/clashed sets: 98 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241699 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241699 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241699/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241699 Building REAL300025241700 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241700' /scratch/stefan/7787021/working/building/REAL300025241700 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241700 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241700/0 /scratch/stefan/7787021/working/building/REAL300025241700 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/579 `/scratch/stefan/7787021/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOCCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241700.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241700 none C=CCOCCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 171, 170, 126, 163, 83, 83, 83, 66, 66, 51, 50, 51, 43, 48, 25, 43, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 143, 164, 163, 163, 163, 163, 83, 66, 66, 66, 66, 51, 51, 51, 51, 50, 50, 50, 25, 25, 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: 1064 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241700 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241700 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241700/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241700 Building REAL300025241701 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241701' /scratch/stefan/7787021/working/building/REAL300025241701 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241701 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241701/0 /scratch/stefan/7787021/working/building/REAL300025241701 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/580 `/scratch/stefan/7787021/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241701.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241701 none CC(CCNC(=O)CC1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 45, 55, 65, 66, 66, 66, 134, 201, 201, 201, 44, 44, 22, 44, 13, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 55, 55, 65, 65, 66, 134, 134, 201, 201, 201, 201, 201, 201, 201, 44, 44, 44, 22, 22, 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: 886 number of broken/clashed sets: 141 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241701 none CC(CCNC(=O)CC1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 26, 17, 17, 5, 17, 1, 1, 1, 1, 1, 37, 42, 42, 44, 44, 80, 120, 201, 201, 201, 201, 201, 37, 37, 37, 37, 35, 35, 26, 26, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 80, 80, 201] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 40, 41, 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, 34, 42, 43, 44, 45, 46, 47]) total number of confs: 581 number of broken/clashed sets: 141 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241701 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241701 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241701/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241701 Building REAL300025241702 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241702' /scratch/stefan/7787021/working/building/REAL300025241702 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241702 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241702/0 /scratch/stefan/7787021/working/building/REAL300025241702 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/581 `/scratch/stefan/7787021/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=CC(=O)N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241702.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241702 none CC(CCNC(=O)C1=CC=CC(=O)N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 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: [98, 87, 98, 103, 108, 108, 108, 108, 201, 201, 201, 201, 201, 201, 68, 87, 28, 68, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 103, 103, 108, 108, 108, 201, 201, 201, 201, 87, 87, 87, 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: 568 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241702 none CC(CCNC(=O)C1=CC=CC(=O)N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 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: [20, 16, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 20, 23, 23, 28, 28, 61, 103, 201, 201, 201, 201, 201, 20, 20, 20, 20, 17, 17, 13, 13, 7, 1, 1, 1, 1, 23, 23, 23, 61, 61, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44]) total number of confs: 511 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241702 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241702 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241702/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241702 Building REAL300025241703 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241703' /scratch/stefan/7787021/working/building/REAL300025241703 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241703 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241703/0 /scratch/stefan/7787021/working/building/REAL300025241703 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/582 `/scratch/stefan/7787021/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1C(C)(C)C1(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241703.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241703 none CC(CCNC(=O)C1C(C)(C)C1(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 86, 101, 120, 128, 129, 129, 129, 201, 201, 201, 201, 201, 201, 60, 86, 28, 60, 13, 1, 1, 1, 1, 1, 1, 1, 101, 101, 101, 101, 120, 120, 128, 128, 129, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 86, 86, 86, 28, 28, 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: 794 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: REAL300025241703 none CC(CCNC(=O)C1C(C)(C)C1(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 14, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 20, 25, 25, 33, 33, 65, 101, 201, 201, 201, 201, 201, 20, 20, 20, 20, 15, 15, 12, 12, 5, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 25, 25, 25, 65, 65, 201] 201 rigid atoms, others: [35, 5, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 540 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241703 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241703 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241703/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241703 Building REAL300025241704 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241704' /scratch/stefan/7787021/working/building/REAL300025241704 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241704 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241704/0 /scratch/stefan/7787021/working/building/REAL300025241704 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/583 `/scratch/stefan/7787021/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)OC=N1) `REAL300025241704.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241704 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 159, 159, 148, 132, 109, 93, 109, 66, 93, 27, 66, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 159, 148, 148, 132, 132, 109, 109, 109, 109, 93, 93, 93, 27, 27, 1, 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]) total number of confs: 724 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241704 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 14, 23, 23, 29, 29, 39, 39, 77, 122, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 3, 9, 9, 14, 14, 23, 23, 23, 23, 29, 29, 29, 77, 77, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 43, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 575 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241704 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241704 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241704/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241704 Building REAL300025241705 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241705' /scratch/stefan/7787021/working/building/REAL300025241705 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241705 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241705/0 /scratch/stefan/7787021/working/building/REAL300025241705 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/584 `/scratch/stefan/7787021/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C(C)C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241705.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241705 none CC(CCNC(=O)C(C)C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 82, 85, 93, 98, 98, 98, 98, 201, 201, 201, 201, 69, 82, 26, 68, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 93, 93, 98, 98, 98, 201, 201, 201, 201, 201, 201, 201, 201, 201, 82, 82, 82, 26, 26, 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: 829 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241705 none CC(CCNC(=O)C(C)C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 15, 9, 9, 2, 9, 1, 2, 1, 1, 1, 24, 24, 24, 30, 30, 69, 115, 201, 201, 201, 201, 201, 24, 24, 24, 24, 18, 18, 15, 15, 9, 2, 2, 2, 2, 1, 1, 1, 1, 1, 24, 24, 24, 69, 69, 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]) total number of confs: 533 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241705 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241705 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241705/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241705 Building REAL300025241706 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241706' /scratch/stefan/7787021/working/building/REAL300025241706 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241706 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241706/0 /scratch/stefan/7787021/working/building/REAL300025241706 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/585 `/scratch/stefan/7787021/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1C2CCCC21)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241706.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241706 none CC(CCNC(=O)C1C2CCCC21)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [111, 93, 111, 125, 139, 150, 150, 150, 201, 201, 201, 201, 201, 62, 93, 28, 61, 13, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 125, 125, 139, 139, 150, 201, 201, 201, 201, 201, 201, 201, 201, 201, 93, 93, 93, 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: 801 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: REAL300025241706 none CC(CCNC(=O)C1C2CCCC21)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [16, 12, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 16, 24, 24, 34, 34, 62, 103, 201, 201, 201, 201, 201, 16, 16, 16, 16, 12, 12, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 62, 62, 201] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 496 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241706 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241706 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241706/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241706 Building REAL300025241707 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241707' /scratch/stefan/7787021/working/building/REAL300025241707 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241707 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241707/0 /scratch/stefan/7787021/working/building/REAL300025241707 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/586 `/scratch/stefan/7787021/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC(C#N)=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241707.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241707 none CC(CCNC(=O)C1=CC(C#N)=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 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: [123, 108, 123, 149, 170, 190, 190, 190, 201, 201, 201, 201, 201, 201, 74, 108, 28, 74, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 149, 149, 170, 170, 190, 201, 201, 201, 108, 108, 108, 28, 28, 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: 787 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241707 none CC(CCNC(=O)C1=CC(C#N)=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 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, 13, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 17, 24, 24, 34, 34, 69, 108, 201, 201, 201, 201, 201, 17, 17, 17, 17, 13, 13, 12, 12, 5, 1, 1, 1, 24, 24, 24, 69, 69, 201] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 514 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241707 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241707 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241707/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241707 Building REAL300025241708 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241708' /scratch/stefan/7787021/working/building/REAL300025241708 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241708 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241708/0 /scratch/stefan/7787021/working/building/REAL300025241708 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/587 `/scratch/stefan/7787021/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241708.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241708 none CC1=CSC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 1, 1, 14, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 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, 7, 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: [201, 201, 201, 201, 201, 125, 125, 125, 125, 115, 101, 87, 101, 65, 87, 25, 64, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 125, 125, 125, 115, 115, 101, 101, 101, 101, 87, 87, 87, 25, 25, 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: 627 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: REAL300025241708 none CC1=CSC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 1, 1, 14, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 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, 7, 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, 1, 1, 1, 7, 7, 7, 12, 14, 23, 23, 29, 29, 37, 37, 75, 122, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 7, 12, 12, 15, 15, 23, 23, 23, 23, 29, 29, 29, 75, 75, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241708 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241708 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241708/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241708 Building REAL300025241709 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241709' /scratch/stefan/7787021/working/building/REAL300025241709 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241709 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241709/0 /scratch/stefan/7787021/working/building/REAL300025241709 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/588 `/scratch/stefan/7787021/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241709.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241709 none CC(CCNC(=O)CCC1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 48, 48, 48, 48, 48, 130, 130, 201, 201, 201, 45, 45, 26, 45, 13, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 48, 48, 48, 48, 48, 130, 130, 145, 145, 201, 201, 201, 201, 201, 201, 201, 45, 45, 45, 26, 26, 1] 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]) total number of confs: 894 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241709 none CC(CCNC(=O)CCC1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 26, 26, 7, 26, 5, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 73, 118, 201, 201, 201, 201, 201, 30, 30, 30, 30, 30, 30, 30, 30, 26, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 73, 73, 201] 201 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 44, 40, 41, 42] 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, 37, 45, 46, 47, 48, 49, 50]) total number of confs: 537 number of broken/clashed sets: 165 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241709 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241709 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241709/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241709 Building REAL300025241710 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241710' /scratch/stefan/7787021/working/building/REAL300025241710 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241710 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241710/0 /scratch/stefan/7787021/working/building/REAL300025241710 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/589 `/scratch/stefan/7787021/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)O1) `REAL300025241710.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241710 none CC1=CC(C)=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 144, 144, 144, 140, 123, 95, 80, 95, 58, 80, 26, 57, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 144, 140, 140, 123, 123, 95, 95, 95, 95, 80, 80, 80, 26, 26, 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: 722 number of broken/clashed sets: 83 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241710 none CC1=CC(C)=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 14, 23, 23, 29, 29, 43, 43, 84, 124, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 2, 2, 2, 3, 9, 9, 14, 14, 23, 23, 23, 23, 29, 29, 29, 84, 84, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 29] set([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, 45, 46, 47]) total number of confs: 603 number of broken/clashed sets: 83 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241710 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241710 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241710/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241710 Building REAL300025241711 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241711' /scratch/stefan/7787021/working/building/REAL300025241711 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241711 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241711/0 /scratch/stefan/7787021/working/building/REAL300025241711 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/590 `/scratch/stefan/7787021/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1=NN=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241711.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241711 none CC(CCNC(=O)CCC1=NN=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 58, 61, 70, 99, 135, 135, 135, 201, 201, 201, 201, 201, 201, 48, 58, 22, 48, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 70, 70, 99, 99, 135, 201, 201, 201, 201, 201, 201, 58, 58, 58, 22, 22, 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: 879 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: REAL300025241711 none CC(CCNC(=O)CCC1=NN=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [28, 24, 20, 9, 9, 5, 9, 5, 1, 1, 1, 1, 1, 1, 28, 29, 29, 34, 34, 66, 104, 201, 201, 201, 201, 201, 28, 28, 28, 28, 24, 24, 20, 20, 9, 5, 5, 5, 5, 1, 1, 29, 29, 29, 66, 66, 201] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 530 number of broken/clashed sets: 109 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241711 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241711/1 /scratch/stefan/7787021/working/building/REAL300025241711 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/591 `/scratch/stefan/7787021/working/3D/591' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1=NNC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241711.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241711/1/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: REAL300025241711 none CC(CCNC(=O)CCC1=NNC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 59, 70, 84, 95, 99, 99, 99, 140, 140, 201, 201, 201, 201, 58, 59, 26, 58, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 84, 84, 95, 95, 99, 140, 140, 140, 140, 201, 201, 59, 59, 59, 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: 761 number of broken/clashed sets: 133 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241711 none CC(CCNC(=O)CCC1=NNC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 18, 11, 11, 8, 11, 7, 1, 1, 1, 1, 1, 1, 19, 23, 23, 26, 26, 62, 99, 201, 201, 201, 201, 201, 19, 19, 19, 19, 18, 18, 18, 18, 11, 8, 8, 7, 7, 1, 1, 23, 23, 23, 62, 62, 201] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 526 number of broken/clashed sets: 133 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241711 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241711 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241711/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241711/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241711 Building REAL300025241712 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241712' /scratch/stefan/7787021/working/building/REAL300025241712 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241712 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241712/0 /scratch/stefan/7787021/working/building/REAL300025241712 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/592 `/scratch/stefan/7787021/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CN=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241712.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241712 none CC1=CC=CN=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 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, 7] 0 hydrogens need 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, 160, 160, 160, 137, 121, 99, 76, 99, 51, 76, 22, 51, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 160, 137, 137, 121, 121, 99, 99, 99, 99, 76, 76, 76, 22, 22, 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: 754 number of broken/clashed sets: 101 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241712 none CC1=CC=CN=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations 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, 15, 19, 28, 28, 38, 38, 49, 49, 90, 127, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 4, 15, 15, 20, 20, 28, 28, 28, 28, 38, 38, 38, 90, 90, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 625 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241712 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241712 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241712/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241712 Building REAL300025241713 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241713' /scratch/stefan/7787021/working/building/REAL300025241713 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241713 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241713/0 /scratch/stefan/7787021/working/building/REAL300025241713 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/593 `/scratch/stefan/7787021/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241713.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241713 none CC=C(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 201, 162, 162, 162, 150, 136, 114, 136, 79, 114, 28, 78, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 162, 162, 162, 150, 150, 136, 136, 136, 136, 114, 114, 114, 28, 28, 1] 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]) total number of confs: 750 number of broken/clashed sets: 119 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241713 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241713 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241713/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241713 Building REAL300025241714 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241714' /scratch/stefan/7787021/working/building/REAL300025241714 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241714 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241714/0 /scratch/stefan/7787021/working/building/REAL300025241714 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/594 `/scratch/stefan/7787021/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1CCOC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241714.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241714 none CC(CCNC(=O)CCC1CCOC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 64, 64, 64, 64, 168, 188, 201, 201, 201, 201, 52, 62, 24, 51, 12, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 62, 62, 64, 64, 64, 168, 168, 197, 197, 201, 201, 201, 201, 201, 201, 201, 62, 62, 62, 24, 24, 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: 823 number of broken/clashed sets: 142 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241714 none CC(CCNC(=O)CCC1CCOC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 24, 5, 24, 3, 1, 1, 1, 1, 1, 1, 25, 25, 25, 27, 27, 69, 109, 201, 201, 201, 201, 201, 25, 25, 25, 25, 25, 25, 24, 24, 24, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 69, 69, 201] 201 rigid atoms, others: [45, 43, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 49, 50, 51]) total number of confs: 509 number of broken/clashed sets: 142 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241714 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241714 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241714/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241714 Building REAL300025241715 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241715' /scratch/stefan/7787021/working/building/REAL300025241715 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241715 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241715/0 /scratch/stefan/7787021/working/building/REAL300025241715 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/595 `/scratch/stefan/7787021/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1=COC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241715.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241715 none CC(CCNC(=O)CCC1=COC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 1, 1, 12, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [55, 55, 55, 55, 63, 64, 64, 64, 131, 131, 201, 201, 201, 201, 47, 55, 23, 46, 13, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 63, 63, 64, 131, 131, 131, 131, 201, 201, 201, 55, 55, 55, 23, 23, 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: 644 number of broken/clashed sets: 140 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241715 none CC(CCNC(=O)CCC1=COC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 1, 1, 12, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [35, 34, 29, 21, 21, 5, 21, 2, 1, 1, 1, 1, 1, 1, 35, 35, 35, 36, 36, 76, 117, 201, 201, 201, 201, 201, 35, 35, 35, 35, 34, 34, 29, 29, 21, 5, 5, 2, 2, 1, 1, 1, 35, 35, 35, 76, 76, 201] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46, 47]) total number of confs: 555 number of broken/clashed sets: 141 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241715 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241715 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241715/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241715 Building REAL300025241716 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241716' /scratch/stefan/7787021/working/building/REAL300025241716 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241716 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241716/0 /scratch/stefan/7787021/working/building/REAL300025241716 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/596 `/scratch/stefan/7787021/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CC(F)(F)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241716.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241716 none CC(CCNC(=O)C1CC(F)(F)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [94, 89, 94, 98, 103, 103, 103, 103, 201, 201, 201, 201, 201, 70, 89, 28, 69, 13, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 98, 98, 103, 103, 103, 201, 201, 201, 201, 201, 89, 89, 89, 28, 28, 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: 692 number of broken/clashed sets: 99 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241716 none CC(CCNC(=O)C1CC(F)(F)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [24, 18, 15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 25, 25, 33, 33, 72, 115, 201, 201, 201, 201, 201, 24, 24, 24, 24, 18, 18, 15, 15, 9, 1, 1, 1, 1, 1, 25, 25, 25, 72, 72, 201] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44]) total number of confs: 541 number of broken/clashed sets: 99 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241716 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241716 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241716/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241716 Building REAL300025241717 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241717' /scratch/stefan/7787021/working/building/REAL300025241717 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241717 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241717/0 /scratch/stefan/7787021/working/building/REAL300025241717 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/597 `/scratch/stefan/7787021/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CC(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241717.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241717 none CC(CCNC(=O)C1CC(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 80, 87, 90, 94, 95, 95, 95, 201, 201, 201, 201, 65, 80, 24, 65, 12, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 90, 90, 94, 94, 95, 201, 201, 201, 201, 201, 201, 201, 201, 201, 80, 80, 80, 24, 24, 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: 671 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241717 none CC(CCNC(=O)C1CC(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 16, 8, 8, 1, 8, 1, 1, 1, 1, 1, 23, 26, 26, 32, 32, 71, 122, 201, 201, 201, 201, 201, 23, 23, 23, 23, 19, 19, 16, 16, 8, 1, 1, 1, 1, 2, 2, 2, 1, 1, 26, 26, 26, 71, 71, 201] 201 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 40, 41] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 42, 43, 44, 45, 46, 47]) total number of confs: 546 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241717 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241717 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241717/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241717 Building REAL300025241718 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241718' /scratch/stefan/7787021/working/building/REAL300025241718 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241718 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241718/0 /scratch/stefan/7787021/working/building/REAL300025241718 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/598 `/scratch/stefan/7787021/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)=C1CCCC1) `REAL300025241718.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241718 none CC(C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 8, 17, 18, 24, 24, 28, 28, 32, 32, 62, 99, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 2, 8, 17, 17, 19, 19, 24, 24, 24, 24, 28, 28, 28, 62, 62, 201, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 44, 45, 46, 47, 48, 49, 50, 51, 21, 22, 23, 24, 25] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 517 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: REAL300025241718 none CC(C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 154, 154, 154, 146, 137, 114, 94, 114, 63, 94, 31, 63, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 154, 146, 146, 137, 137, 114, 114, 114, 114, 94, 94, 94, 31, 31, 1, 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]) total number of confs: 770 number of broken/clashed sets: 123 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241718 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241718 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241718/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241718 Building REAL300025241719 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241719' /scratch/stefan/7787021/working/building/REAL300025241719 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241719 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241719/0 /scratch/stefan/7787021/working/building/REAL300025241719 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/599 `/scratch/stefan/7787021/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1CCCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241719.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241719 none CC(CCNC(=O)CC1CCCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 51, 55, 77, 92, 101, 101, 101, 176, 201, 201, 201, 201, 201, 51, 51, 28, 51, 13, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 77, 77, 92, 92, 101, 176, 176, 201, 201, 201, 201, 201, 201, 201, 201, 201, 51, 51, 51, 28, 28, 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: 836 number of broken/clashed sets: 144 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241719 none CC(CCNC(=O)CC1CCCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 14, 14, 6, 14, 1, 1, 1, 1, 1, 1, 1, 33, 36, 36, 37, 37, 72, 105, 201, 201, 201, 201, 201, 33, 33, 33, 33, 26, 26, 21, 21, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 72, 72, 201] 201 rigid atoms, others: [45, 11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 44, 40, 43, 41, 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, 46, 47, 48, 49, 50, 51]) total number of confs: 555 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241719 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241719 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241719/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241719 Building REAL300025241720 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241720' /scratch/stefan/7787021/working/building/REAL300025241720 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241720 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241720/0 /scratch/stefan/7787021/working/building/REAL300025241720 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/600 `/scratch/stefan/7787021/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=NN1) `REAL300025241720.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241720 none CC1=CC(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 201, 80, 80, 80, 78, 78, 55, 53, 55, 39, 54, 28, 39, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 80, 78, 78, 78, 78, 55, 55, 55, 55, 54, 54, 54, 28, 28, 1, 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]) total number of confs: 861 number of broken/clashed sets: 89 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241720 none CC1=CC(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 3, 9, 9, 9, 15, 15, 19, 19, 19, 19, 41, 41, 57, 95, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 3, 3, 9, 15, 15, 15, 15, 19, 19, 19, 19, 19, 19, 19, 57, 57, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 47, 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, 45, 46]) total number of confs: 506 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241720 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241720/1 /scratch/stefan/7787021/working/building/REAL300025241720 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/601 `/scratch/stefan/7787021/working/3D/601' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1) `REAL300025241720.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241720/1/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: REAL300025241720 none CC1=NNC(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7] 0 hydrogens need 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, 114, 114, 114, 106, 105, 77, 67, 77, 50, 68, 38, 50, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 114, 106, 106, 105, 105, 77, 77, 77, 77, 68, 68, 68, 38, 38, 1, 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]) total number of confs: 952 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241720 none CC1=NNC(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 12, 12, 12, 22, 22, 23, 23, 25, 25, 48, 48, 65, 99, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 5, 5, 12, 22, 22, 22, 22, 23, 23, 23, 23, 25, 25, 25, 65, 65, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 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, 45, 46]) total number of confs: 515 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241720 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241720 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241720/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241720/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241720 Building REAL300025241721 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241721' /scratch/stefan/7787021/working/building/REAL300025241721 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241721 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241721/0 /scratch/stefan/7787021/working/building/REAL300025241721 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/602 `/scratch/stefan/7787021/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C=C1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241721.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241721 none CC(CCNC(=O)C=C1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7] 0 hydrogens 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, 94, 104, 108, 113, 114, 114, 114, 201, 201, 201, 201, 71, 94, 27, 70, 13, 1, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 108, 108, 113, 113, 114, 201, 201, 201, 201, 201, 201, 201, 94, 94, 94, 27, 27, 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: 734 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241721 none CC(CCNC(=O)C=C1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7] 0 hydrogens 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, 13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 19, 24, 24, 28, 28, 64, 100, 201, 201, 201, 201, 201, 19, 19, 19, 19, 15, 15, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 64, 64, 201] 201 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45]) total number of confs: 507 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241721 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241721 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241721/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241721 Building REAL300025241722 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241722' /scratch/stefan/7787021/working/building/REAL300025241722 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241722 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241722/0 /scratch/stefan/7787021/working/building/REAL300025241722 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/603 `/scratch/stefan/7787021/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CN=CC(F)=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241722.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241722 none CC(CCNC(=O)C1=CN=CC(F)=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 8, 1, 1, 15, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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] 0 hydrogens 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, 58, 67, 71, 75, 75, 75, 75, 201, 201, 201, 201, 201, 201, 49, 58, 24, 48, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 71, 71, 75, 75, 75, 201, 201, 201, 58, 58, 58, 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: 473 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241722 none CC(CCNC(=O)C1=CN=CC(F)=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 8, 1, 1, 15, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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] 0 hydrogens 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, 12, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 17, 21, 21, 26, 26, 54, 93, 201, 201, 201, 201, 201, 17, 17, 17, 17, 13, 13, 11, 11, 5, 1, 1, 1, 21, 21, 21, 54, 54, 201] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 475 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241722 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241722 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241722/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241722 Building REAL300025241723 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241723' /scratch/stefan/7787021/working/building/REAL300025241723 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241723 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241723/0 /scratch/stefan/7787021/working/building/REAL300025241723 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/604 `/scratch/stefan/7787021/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)CC) `REAL300025241723.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241723 none CCC(=CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 143, 143, 98, 98, 98, 98, 91, 80, 68, 80, 46, 68, 23, 45, 13, 1, 1, 1, 1, 1, 1, 1, 143, 187, 189, 189, 189, 189, 189, 143, 98, 98, 98, 91, 91, 80, 80, 80, 80, 68, 68, 68, 23, 23, 1, 187, 187, 187, 187, 187] 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]) total number of confs: 1066 number of broken/clashed sets: 124 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241723 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241723 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241723/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241723 Building REAL300025241724 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241724' /scratch/stefan/7787021/working/building/REAL300025241724 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241724 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241724/0 /scratch/stefan/7787021/working/building/REAL300025241724 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/605 `/scratch/stefan/7787021/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC(=O)NC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241724.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241724 none CC(CCNC(=O)C1=CC(=O)NC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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: [82, 67, 82, 86, 90, 90, 90, 90, 201, 201, 201, 201, 201, 201, 50, 67, 28, 50, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 86, 86, 90, 90, 90, 201, 201, 201, 201, 67, 67, 67, 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: 527 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: REAL300025241724 none CC(CCNC(=O)C1=CC(=O)NC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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: [18, 13, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 18, 23, 23, 27, 27, 54, 89, 201, 201, 201, 201, 201, 18, 18, 18, 18, 14, 14, 12, 12, 5, 1, 1, 1, 1, 23, 23, 23, 54, 54, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44]) total number of confs: 480 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241724 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241724 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241724/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241724 Building REAL300025241725 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241725' /scratch/stefan/7787021/working/building/REAL300025241725 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241725 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241725/0 /scratch/stefan/7787021/working/building/REAL300025241725 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/606 `/scratch/stefan/7787021/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(F)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241725.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241725 none CC(C)=C(F)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 15, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need 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, 128, 201, 128, 128, 125, 117, 105, 94, 105, 61, 94, 23, 61, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 128, 125, 125, 117, 117, 105, 105, 105, 105, 94, 94, 94, 23, 23, 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: 755 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241725 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241725 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241725/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241725 Building REAL300025241726 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241726' /scratch/stefan/7787021/working/building/REAL300025241726 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241726 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241726/0 /scratch/stefan/7787021/working/building/REAL300025241726 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/607 `/scratch/stefan/7787021/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCNC(=O)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241726.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241726 none CC(CCNC(=O)C1CCNC(=O)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 94, 102, 106, 114, 114, 114, 114, 201, 201, 201, 201, 201, 201, 71, 94, 28, 70, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 102, 102, 106, 106, 114, 114, 114, 201, 201, 201, 201, 201, 201, 201, 201, 94, 94, 94, 28, 28, 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: 695 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: REAL300025241726 none CC(CCNC(=O)C1CCNC(=O)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 18, 21, 21, 28, 28, 68, 109, 201, 201, 201, 201, 201, 18, 18, 18, 18, 15, 15, 13, 13, 7, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 68, 68, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 39, 12, 13, 11, 40, 41, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46, 47, 48]) total number of confs: 513 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241726 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241726 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241726/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241726 Building REAL300025241727 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241727' /scratch/stefan/7787021/working/building/REAL300025241727 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241727 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241727/0 /scratch/stefan/7787021/working/building/REAL300025241727 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/608 `/scratch/stefan/7787021/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241727.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241727 none CC(CCNC(=O)C1=CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7] 0 hydrogens 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, 112, 145, 175, 193, 201, 201, 201, 201, 201, 201, 201, 79, 112, 33, 78, 13, 1, 1, 1, 1, 1, 1, 1, 145, 145, 145, 145, 175, 175, 193, 193, 201, 201, 201, 201, 201, 201, 201, 201, 112, 112, 112, 33, 33, 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: 831 number of broken/clashed sets: 121 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241727 none CC(CCNC(=O)C1=CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7] 0 hydrogens 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, 18, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 28, 34, 34, 44, 44, 83, 121, 201, 201, 201, 201, 201, 28, 28, 28, 28, 20, 20, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 83, 83, 201] 201 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45]) total number of confs: 580 number of broken/clashed sets: 121 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241727 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241727 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241727/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241727 Building REAL300025241728 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241728' /scratch/stefan/7787021/working/building/REAL300025241728 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241728 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241728/0 /scratch/stefan/7787021/working/building/REAL300025241728 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/609 `/scratch/stefan/7787021/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C(F)=C1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241728.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241728 none CC(CCNC(=O)C(F)=C1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 15, 1, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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: [133, 114, 133, 156, 175, 178, 178, 178, 201, 201, 201, 201, 201, 201, 73, 114, 30, 73, 13, 1, 1, 1, 1, 1, 1, 1, 133, 133, 133, 133, 156, 156, 175, 175, 178, 201, 201, 201, 201, 201, 201, 201, 201, 114, 114, 114, 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: 815 number of broken/clashed sets: 89 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241728 none CC(CCNC(=O)C(F)=C1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 15, 1, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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: [19, 12, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 19, 26, 26, 35, 35, 76, 115, 201, 201, 201, 201, 201, 19, 19, 19, 19, 12, 12, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 76, 76, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46, 47, 48]) total number of confs: 551 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241728 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241728 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241728/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241728 Building REAL300025241729 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241729' /scratch/stefan/7787021/working/building/REAL300025241729 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241729 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241729/0 /scratch/stefan/7787021/working/building/REAL300025241729 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/610 `/scratch/stefan/7787021/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CN(C)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241729.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241729 none CC(CCNC(=O)C1=CN(C)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [119, 105, 119, 125, 130, 130, 130, 130, 201, 201, 201, 201, 201, 80, 105, 28, 79, 13, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 125, 125, 130, 130, 130, 201, 201, 201, 201, 201, 201, 105, 105, 105, 28, 28, 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: 603 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241729 none CC(CCNC(=O)C1=CN(C)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [20, 16, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 20, 28, 28, 32, 32, 73, 118, 201, 201, 201, 201, 201, 20, 20, 20, 20, 17, 17, 11, 11, 5, 1, 2, 2, 2, 1, 1, 28, 28, 28, 73, 73, 201] 201 rigid atoms, others: [34, 5, 38, 7, 8, 9, 10, 11, 12, 39] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 547 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241729 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241729 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241729/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241729 Building REAL300025241730 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241730' /scratch/stefan/7787021/working/building/REAL300025241730 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241730 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241730/0 /scratch/stefan/7787021/working/building/REAL300025241730 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/611 `/scratch/stefan/7787021/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CN(C)C=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241730.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241730 none CC(CCNC(=O)C1=CN(C)C=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 1, 8, 5, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [122, 108, 122, 162, 178, 201, 201, 201, 201, 201, 201, 201, 201, 64, 108, 26, 64, 13, 1, 1, 1, 1, 1, 1, 1, 122, 122, 122, 122, 162, 162, 178, 178, 201, 201, 201, 201, 201, 201, 108, 108, 108, 26, 26, 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: 830 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: REAL300025241730 none CC(CCNC(=O)C1=CN(C)C=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 1, 8, 5, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [14, 9, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 20, 20, 35, 35, 67, 107, 201, 201, 201, 201, 201, 14, 14, 14, 14, 9, 9, 7, 7, 2, 1, 2, 2, 2, 1, 20, 20, 20, 67, 67, 201] 201 rigid atoms, others: [34, 5, 38, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 517 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241730 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241730 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241730/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241730 Building REAL300025241731 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241731' /scratch/stefan/7787021/working/building/REAL300025241731 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241731 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241731/0 /scratch/stefan/7787021/working/building/REAL300025241731 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/612 `/scratch/stefan/7787021/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1COC(=O)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241731.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241731 none CC(CCNC(=O)CC1COC(=O)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 5, 12, 1, 11, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 90, 92, 92, 92, 197, 201, 201, 201, 201, 201, 76, 86, 28, 76, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 86, 86, 90, 90, 92, 197, 197, 201, 201, 201, 201, 201, 86, 86, 86, 28, 28, 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: 778 number of broken/clashed sets: 111 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241731 none CC(CCNC(=O)CC1COC(=O)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 5, 12, 1, 11, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 22, 22, 6, 22, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 31, 31, 69, 113, 201, 201, 201, 201, 201, 27, 27, 27, 27, 27, 27, 26, 26, 22, 6, 6, 1, 1, 1, 1, 1, 27, 27, 27, 69, 69, 201] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 40, 41] 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, 42, 43, 44, 45, 46, 47]) total number of confs: 497 number of broken/clashed sets: 111 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241731 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241731 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241731/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241731 Building REAL300025241732 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241732' /scratch/stefan/7787021/working/building/REAL300025241732 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241732 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241732/0 /scratch/stefan/7787021/working/building/REAL300025241732 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/613 `/scratch/stefan/7787021/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)OC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1) `REAL300025241732.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241732 none CC1=C(C)OC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 5, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need 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, 181, 157, 117, 99, 117, 66, 99, 27, 66, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 181, 181, 157, 157, 117, 117, 117, 117, 99, 99, 99, 27, 27, 1, 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]) total number of confs: 850 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: REAL300025241732 none CC1=C(C)OC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 5, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 1, 1, 7, 9, 17, 17, 25, 25, 36, 36, 65, 100, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 6, 6, 10, 10, 17, 17, 17, 17, 25, 25, 25, 65, 65, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 47, 32, 25, 29, 30, 31] set([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]) total number of confs: 513 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241732 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241732 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241732/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241732 Building REAL300025241733 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241733' /scratch/stefan/7787021/working/building/REAL300025241733 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241733 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241733/0 /scratch/stefan/7787021/working/building/REAL300025241733 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/614 `/scratch/stefan/7787021/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1=CC=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241733.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241733 none CC(CCNC(=O)CC1=CC=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [59, 58, 59, 59, 59, 63, 63, 63, 152, 201, 201, 201, 201, 201, 49, 58, 24, 48, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 63, 152, 152, 201, 201, 201, 201, 58, 58, 58, 24, 24, 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: 687 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241733 none CC(CCNC(=O)CC1=CC=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 14, 15, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 21, 21, 54, 91, 201, 201, 201, 201, 201, 15, 15, 15, 15, 15, 15, 15, 15, 9, 3, 3, 1, 1, 1, 1, 15, 15, 15, 54, 54, 201] 201 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 13, 40, 39] 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, 41, 42, 43, 44, 45, 46]) total number of confs: 478 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241733 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241733 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241733/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241733 Building REAL300025241734 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241734' /scratch/stefan/7787021/working/building/REAL300025241734 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241734 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241734/0 /scratch/stefan/7787021/working/building/REAL300025241734 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/615 `/scratch/stefan/7787021/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241734.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241734 none CC(CCNC(=O)C1CCCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 83, 103, 130, 147, 166, 166, 166, 201, 201, 201, 201, 201, 56, 83, 27, 56, 13, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 130, 130, 147, 147, 166, 201, 201, 201, 201, 201, 201, 201, 201, 201, 83, 83, 83, 27, 27, 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: 841 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: REAL300025241734 none CC(CCNC(=O)C1CCCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 15, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 30, 38, 38, 49, 49, 82, 116, 201, 201, 201, 201, 201, 30, 30, 30, 30, 21, 21, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 82, 82, 201] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 579 number of broken/clashed sets: 102 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241734 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241734 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241734/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241734 Building REAL300025241735 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241735' /scratch/stefan/7787021/working/building/REAL300025241735 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241735 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241735/0 /scratch/stefan/7787021/working/building/REAL300025241735 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/616 `/scratch/stefan/7787021/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C1=O) `REAL300025241735.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241735 none CC1=NNC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 139, 139, 139, 137, 125, 116, 103, 116, 78, 103, 30, 77, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 139, 137, 137, 125, 125, 116, 116, 116, 116, 103, 103, 103, 30, 30, 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: 747 number of broken/clashed sets: 99 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241735 none CC1=NNC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 11, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 11, 11, 11, 19, 20, 22, 22, 24, 24, 31, 31, 74, 116, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 11, 19, 19, 20, 20, 22, 22, 22, 22, 24, 24, 24, 74, 74, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 531 number of broken/clashed sets: 99 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241735 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241735 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241735/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241735 Building REAL300025241736 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241736' /scratch/stefan/7787021/working/building/REAL300025241736 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241736 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241736/0 /scratch/stefan/7787021/working/building/REAL300025241736 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/617 `/scratch/stefan/7787021/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(SC)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241736.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241736 none CCC(SC)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 187, 177, 187, 201, 177, 177, 161, 140, 113, 92, 113, 60, 92, 28, 59, 13, 1, 1, 1, 1, 1, 1, 1, 188, 188, 188, 188, 188, 187, 201, 201, 201, 177, 161, 161, 140, 140, 113, 113, 113, 113, 92, 92, 92, 28, 28, 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: 845 number of broken/clashed sets: 118 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241736 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241736 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241736/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241736 Building REAL300025241737 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241737' /scratch/stefan/7787021/working/building/REAL300025241737 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241737 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241737/0 /scratch/stefan/7787021/working/building/REAL300025241737 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/618 `/scratch/stefan/7787021/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=NC=N1) `REAL300025241737.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241737 none CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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 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, 181, 159, 126, 104, 126, 62, 104, 26, 62, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 181, 181, 159, 159, 126, 126, 126, 126, 104, 104, 104, 26, 26, 1, 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]) total number of confs: 835 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241737 none CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 3, 9, 11, 19, 19, 29, 29, 40, 40, 68, 106, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 3, 9, 9, 12, 12, 19, 19, 19, 19, 29, 29, 29, 68, 68, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 45, 23, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 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: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241737 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241737 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241737/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241737 Building REAL300025241738 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241738' /scratch/stefan/7787021/working/building/REAL300025241738 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241738 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241738/0 /scratch/stefan/7787021/working/building/REAL300025241738 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/619 `/scratch/stefan/7787021/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CC1(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241738.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241738 none CC(CCNC(=O)C1CC1(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 94, 106, 121, 128, 129, 129, 129, 201, 201, 201, 201, 69, 94, 29, 68, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 106, 121, 121, 128, 128, 129, 201, 201, 201, 201, 201, 201, 201, 201, 201, 94, 94, 94, 29, 29, 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: 776 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: REAL300025241738 none CC(CCNC(=O)C1CC1(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 19, 25, 25, 33, 33, 71, 111, 201, 201, 201, 201, 201, 19, 19, 19, 19, 14, 14, 12, 12, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 25, 25, 25, 71, 71, 201] 201 rigid atoms, others: [33, 34, 35, 5, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 545 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241738 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241738 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241738/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241738 Building REAL300025241739 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241739' /scratch/stefan/7787021/working/building/REAL300025241739 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241739 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241739/0 /scratch/stefan/7787021/working/building/REAL300025241739 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/620 `/scratch/stefan/7787021/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)OCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241739.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241739 none CCC(C)OCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 177, 124, 124, 124, 94, 94, 63, 56, 63, 43, 57, 29, 43, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 177, 177, 124, 94, 94, 94, 94, 63, 63, 63, 63, 57, 57, 57, 29, 29, 1] 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]) total number of confs: 833 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241739 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241739 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241739/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241739 Building REAL300025241740 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241740' /scratch/stefan/7787021/working/building/REAL300025241740 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241740 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241740/0 /scratch/stefan/7787021/working/building/REAL300025241740 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/621 `/scratch/stefan/7787021/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)[C@H]1CC1(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241740.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241740 none CC(CCNC(=O)[C@H]1CC1(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 94, 107, 122, 129, 130, 130, 130, 201, 201, 201, 201, 201, 69, 94, 29, 68, 13, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 122, 122, 129, 129, 130, 201, 201, 201, 201, 201, 201, 201, 201, 94, 94, 94, 29, 29, 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: 778 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241740 none CC(CCNC(=O)[C@H]1CC1(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 13, 12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 25, 25, 33, 33, 70, 112, 201, 201, 201, 201, 201, 19, 19, 19, 19, 14, 14, 12, 12, 6, 1, 1, 2, 2, 2, 2, 2, 2, 25, 25, 25, 70, 70, 201] 201 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 545 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241740 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241740 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241740/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241740 Building REAL300025241741 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241741' /scratch/stefan/7787021/working/building/REAL300025241741 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241741 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241741/0 /scratch/stefan/7787021/working/building/REAL300025241741 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/622 `/scratch/stefan/7787021/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC(C)(O)C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241741.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241741 none CC(CCNC(=O)CC(C)(O)C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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, 7, 4, 7, 6, 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: [84, 76, 84, 93, 104, 105, 105, 105, 188, 201, 201, 201, 201, 201, 65, 76, 29, 64, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 93, 93, 104, 104, 105, 188, 188, 201, 201, 201, 603, 201, 201, 201, 201, 201, 76, 76, 76, 29, 29, 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: 335 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241741 none CC(CCNC(=O)CC(C)(O)C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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, 7, 4, 7, 6, 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: [25, 21, 19, 13, 13, 8, 13, 2, 1, 2, 2, 1, 1, 1, 25, 26, 26, 30, 30, 64, 99, 201, 201, 201, 201, 201, 25, 25, 25, 25, 22, 22, 19, 19, 13, 8, 8, 3, 3, 3, 6, 1, 1, 1, 1, 1, 26, 26, 26, 64, 64, 201] 603 rigid atoms, others: [45, 43, 8, 41, 42, 11, 12, 13, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 40, 46, 47, 48, 49, 50, 51]) total number of confs: 532 number of broken/clashed sets: 335 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241741 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241741 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241741/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241741 Building REAL300025241742 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241742' /scratch/stefan/7787021/working/building/REAL300025241742 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241742 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241742/0 /scratch/stefan/7787021/working/building/REAL300025241742 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/623 `/scratch/stefan/7787021/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC(C)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241742.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241742 none CSC(C)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 182, 181, 182, 112, 112, 112, 109, 99, 82, 74, 82, 70, 74, 31, 69, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 182, 182, 182, 182, 181, 181, 112, 109, 109, 99, 99, 82, 82, 82, 82, 74, 74, 74, 31, 31, 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: 837 number of broken/clashed sets: 147 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241742 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241742 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241742/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241742 Building REAL300025241743 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241743' /scratch/stefan/7787021/working/building/REAL300025241743 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241743 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241743/0 /scratch/stefan/7787021/working/building/REAL300025241743 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/624 `/scratch/stefan/7787021/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CN1CCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241743.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241743 none CC(CCNC(=O)CN1CCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7] 0 hydrogens 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, 90, 106, 107, 107, 107, 201, 201, 201, 201, 201, 201, 59, 72, 27, 59, 12, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 90, 90, 106, 106, 107, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 72, 72, 72, 27, 27, 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: 901 number of broken/clashed sets: 101 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241743 none CC(CCNC(=O)CN1CCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7] 0 hydrogens 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, 20, 15, 10, 10, 5, 10, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 36, 36, 72, 109, 201, 201, 201, 201, 201, 26, 26, 26, 26, 20, 20, 15, 15, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 72, 72, 201] 201 rigid atoms, others: [43, 37, 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, 45, 46, 47, 48, 49, 50]) total number of confs: 558 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241743 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241743 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241743/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241743 Building REAL300025241744 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241744' /scratch/stefan/7787021/working/building/REAL300025241744 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241744 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241744/0 /scratch/stefan/7787021/working/building/REAL300025241744 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/625 `/scratch/stefan/7787021/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)[C@@H]1CCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241744.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241744 none CC(CCNC(=O)[C@@H]1CCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [118, 98, 118, 147, 172, 188, 188, 188, 201, 201, 201, 201, 201, 67, 98, 29, 67, 13, 1, 1, 1, 1, 1, 1, 1, 118, 118, 118, 118, 147, 147, 172, 172, 188, 201, 201, 201, 201, 201, 201, 98, 98, 98, 29, 29, 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: 855 number of broken/clashed sets: 98 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241744 none CC(CCNC(=O)[C@@H]1CCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [20, 14, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 20, 30, 30, 38, 38, 73, 110, 201, 201, 201, 201, 201, 20, 20, 20, 20, 15, 15, 14, 14, 5, 1, 1, 1, 1, 1, 1, 30, 30, 30, 73, 73, 201] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45]) total number of confs: 541 number of broken/clashed sets: 98 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241744 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241744 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241744/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241744 Building REAL300025241745 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241745' /scratch/stefan/7787021/working/building/REAL300025241745 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241745 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241745/0 /scratch/stefan/7787021/working/building/REAL300025241745 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/626 `/scratch/stefan/7787021/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C(C)N1C=NC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241745.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241745 none CC(CCNC(=O)C(C)N1C=NC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [74, 73, 74, 91, 122, 139, 139, 139, 201, 201, 201, 201, 201, 201, 61, 73, 26, 60, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 91, 91, 122, 122, 139, 201, 201, 201, 201, 201, 201, 73, 73, 73, 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: 921 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: REAL300025241745 none CC(CCNC(=O)C(C)N1C=NC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [30, 24, 21, 10, 10, 6, 10, 1, 6, 1, 1, 1, 1, 1, 30, 31, 31, 37, 37, 73, 106, 201, 201, 201, 201, 201, 30, 30, 30, 30, 24, 24, 21, 21, 10, 6, 6, 6, 6, 1, 1, 31, 31, 31, 73, 73, 201] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 551 number of broken/clashed sets: 110 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241745 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241745 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241745/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241745 Building REAL300025241746 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241746' /scratch/stefan/7787021/working/building/REAL300025241746 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241746 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241746/0 /scratch/stefan/7787021/working/building/REAL300025241746 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/627 `/scratch/stefan/7787021/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1COCCN1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241746.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241746 none CC(CCNC(=O)C1COCCN1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 10, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 100, 118, 156, 177, 194, 194, 194, 201, 201, 201, 201, 201, 201, 70, 100, 27, 70, 13, 1, 1, 1, 1, 1, 1, 1, 118, 118, 118, 118, 156, 156, 177, 177, 194, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 100, 100, 100, 27, 27, 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: 831 number of broken/clashed sets: 79 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241746 none CC(CCNC(=O)C1COCCN1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 10, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 19, 28, 28, 38, 38, 69, 109, 201, 201, 201, 201, 201, 19, 19, 19, 19, 12, 12, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 28, 28, 28, 69, 69, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 520 number of broken/clashed sets: 79 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241746 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241746 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241746/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241746 Building REAL300025241747 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241747' /scratch/stefan/7787021/working/building/REAL300025241747 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241747 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241747/0 /scratch/stefan/7787021/working/building/REAL300025241747 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/628 `/scratch/stefan/7787021/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NSC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241747.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241747 none CC1=NSC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 1, 8, 14, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 201, 201, 201, 132, 132, 132, 131, 122, 99, 87, 99, 68, 87, 28, 68, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 132, 131, 131, 122, 122, 99, 99, 99, 99, 87, 87, 87, 28, 28, 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: 670 number of broken/clashed sets: 112 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241747 none CC1=NSC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 1, 8, 14, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 6, 6, 6, 13, 15, 24, 24, 28, 28, 36, 36, 74, 119, 201, 201, 201, 201, 201, 2, 2, 2, 1, 6, 13, 13, 16, 16, 24, 24, 24, 24, 28, 28, 28, 74, 74, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241747 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241747 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241747/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241747 Building REAL300025241748 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241748' /scratch/stefan/7787021/working/building/REAL300025241748 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241748 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241748/0 /scratch/stefan/7787021/working/building/REAL300025241748 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/629 `/scratch/stefan/7787021/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241748.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241748 none C#CCCCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 186, 175, 173, 48, 48, 48, 48, 48, 44, 44, 44, 34, 44, 28, 34, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 186, 186, 186, 186, 173, 173, 48, 48, 48, 48, 48, 44, 44, 44, 44, 44, 44, 44, 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: 910 number of broken/clashed sets: 97 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241748 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241748 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241748/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241748 Building REAL300025241749 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241749' /scratch/stefan/7787021/working/building/REAL300025241749 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241749 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241749/0 /scratch/stefan/7787021/working/building/REAL300025241749 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/630 `/scratch/stefan/7787021/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCNC(=O)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241749.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241749 none C#CCNC(=O)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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: [1, 1, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 4, 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, 188, 201, 80, 80, 80, 73, 72, 48, 44, 48, 32, 45, 25, 32, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 188, 188, 80, 73, 73, 72, 72, 48, 48, 48, 48, 45, 45, 45, 25, 25, 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: 870 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241749 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241749 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241749/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241749 Building REAL300025241750 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241750' /scratch/stefan/7787021/working/building/REAL300025241750 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241750 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241750/0 /scratch/stefan/7787021/working/building/REAL300025241750 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/631 `/scratch/stefan/7787021/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241750.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241750 none CCNC(=O)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 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, 4, 7, 6, 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, 7, 7, 7] 0 hydrogens need 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, 71, 71, 71, 68, 67, 50, 45, 50, 32, 46, 25, 32, 11, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 144, 144, 144, 71, 68, 68, 67, 67, 50, 50, 50, 50, 46, 46, 46, 25, 25, 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: 977 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241750 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241750 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241750/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241750 Building REAL300025241751 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241751' /scratch/stefan/7787021/working/building/REAL300025241751 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241751 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241751/0 /scratch/stefan/7787021/working/building/REAL300025241751 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/632 `/scratch/stefan/7787021/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241751.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241751 none CNC(=O)CCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 4, 7, 6, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 153, 146, 44, 44, 44, 44, 44, 36, 36, 36, 27, 36, 23, 27, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 187, 201, 188, 188, 146, 146, 44, 44, 44, 44, 44, 36, 36, 36, 36, 36, 36, 36, 23, 23, 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: 1071 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241751 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241751 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241751/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241751 Building REAL300025241752 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241752' /scratch/stefan/7787021/working/building/REAL300025241752 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241752 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241752/0 /scratch/stefan/7787021/working/building/REAL300025241752 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/633 `/scratch/stefan/7787021/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1) `REAL300025241752.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241752 none COC1=NOC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 3, 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: [201, 201, 201, 201, 201, 197, 197, 197, 141, 135, 110, 75, 110, 61, 75, 40, 61, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 197, 141, 141, 135, 135, 110, 110, 110, 110, 75, 75, 75, 40, 40, 1, 201] 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]) total number of confs: 847 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: REAL300025241752 none COC1=NOC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 3, 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: [2, 1, 1, 1, 1, 1, 1, 5, 5, 4, 12, 14, 21, 21, 34, 34, 55, 55, 76, 112, 201, 201, 201, 201, 201, 1, 3, 3, 3, 5, 12, 12, 14, 14, 21, 21, 21, 21, 34, 34, 34, 76, 76, 201, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 44, 25] set([0, 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: 546 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241752 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241752 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241752/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241752 Building REAL300025241753 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241753' /scratch/stefan/7787021/working/building/REAL300025241753 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241753 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241753/0 /scratch/stefan/7787021/working/building/REAL300025241753 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/634 `/scratch/stefan/7787021/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)CCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241753.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241753 none COC(C)CCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 199, 107, 107, 107, 85, 85, 59, 56, 59, 44, 57, 30, 44, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 107, 85, 85, 85, 85, 59, 59, 59, 59, 57, 57, 57, 30, 30, 1] 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]) total number of confs: 884 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241753 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241753 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241753/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241753 Building REAL300025241754 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241754' /scratch/stefan/7787021/working/building/REAL300025241754 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241754 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241754/0 /scratch/stefan/7787021/working/building/REAL300025241754 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/635 `/scratch/stefan/7787021/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=CO1) `REAL300025241754.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241754 none CCC1=NC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 107, 107, 107, 107, 107, 107, 78, 78, 54, 46, 54, 36, 47, 24, 36, 13, 1, 1, 1, 1, 1, 1, 1, 107, 107, 201, 201, 201, 201, 201, 107, 78, 78, 78, 78, 54, 54, 54, 54, 47, 47, 47, 24, 24, 1, 107] 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]) total number of confs: 1017 number of broken/clashed sets: 89 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241754 none CCC1=NC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 5, 5, 8, 8, 10, 10, 19, 19, 27, 47, 107, 107, 107, 107, 107, 1, 1, 5, 5, 5, 4, 4, 2, 5, 5, 5, 5, 8, 8, 8, 8, 10, 10, 10, 27, 27, 107, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 46, 24, 25] set([0, 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: 268 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241754 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241754 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241754/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241754 Building REAL300025241755 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241755' /scratch/stefan/7787021/working/building/REAL300025241755 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241755 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241755/0 /scratch/stefan/7787021/working/building/REAL300025241755 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/636 `/scratch/stefan/7787021/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=C(F)C=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241755.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241755 none CC(CCNC(=O)C1=CC=C(F)C=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 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: [127, 108, 127, 159, 179, 201, 201, 201, 201, 201, 201, 201, 201, 201, 68, 108, 28, 68, 13, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 159, 159, 179, 179, 201, 201, 201, 201, 108, 108, 108, 28, 28, 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: 826 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: REAL300025241755 none CC(CCNC(=O)C1=CC=C(F)C=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 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, 9, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 26, 26, 38, 38, 68, 106, 201, 201, 201, 201, 201, 17, 17, 17, 17, 10, 10, 7, 7, 1, 1, 1, 1, 26, 26, 26, 68, 68, 201] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 35, 36, 37] set([0, 1, 2, 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]) total number of confs: 526 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241755 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241755 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241755/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241755 Building REAL300025241756 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241756' /scratch/stefan/7787021/working/building/REAL300025241756 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241756 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241756/0 /scratch/stefan/7787021/working/building/REAL300025241756 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/637 `/scratch/stefan/7787021/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=C(N)N(C)N=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241756.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241756 none CC(CCNC(=O)C1=C(N)N(C)N=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 95, 117, 133, 141, 147, 147, 147, 201, 201, 201, 201, 201, 201, 69, 95, 29, 68, 13, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 133, 133, 141, 141, 147, 201, 201, 201, 201, 201, 201, 95, 95, 95, 29, 29, 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: 693 number of broken/clashed sets: 132 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241756 none CC(CCNC(=O)C1=C(N)N(C)N=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 16, 15, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 20, 23, 23, 31, 31, 61, 100, 201, 201, 201, 201, 201, 20, 20, 20, 20, 17, 17, 15, 15, 6, 1, 1, 2, 2, 2, 1, 23, 23, 23, 61, 61, 201] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 40] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 508 number of broken/clashed sets: 132 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241756 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241756 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241756/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241756 Building REAL300025241757 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241757' /scratch/stefan/7787021/working/building/REAL300025241757 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241757 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241757/0 /scratch/stefan/7787021/working/building/REAL300025241757 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/638 `/scratch/stefan/7787021/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CN=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241757.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241757 none CC(CCNC(=O)C1=CN=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 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: [145, 122, 145, 178, 191, 201, 201, 201, 201, 201, 201, 201, 201, 92, 122, 31, 92, 13, 1, 1, 1, 1, 1, 1, 1, 145, 145, 145, 145, 178, 178, 191, 191, 201, 201, 201, 201, 122, 122, 122, 31, 31, 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: 799 number of broken/clashed sets: 105 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241757 none CC(CCNC(=O)C1=CN=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 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: [18, 10, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 18, 25, 25, 32, 32, 71, 121, 201, 201, 201, 201, 201, 18, 18, 18, 18, 12, 12, 10, 10, 3, 1, 1, 1, 25, 25, 25, 71, 71, 201] 201 rigid atoms, others: [34, 35, 36, 5, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 547 number of broken/clashed sets: 137 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241757 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241757 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241757/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241757 Building REAL300025241758 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241758' /scratch/stefan/7787021/working/building/REAL300025241758 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241758 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241758/0 /scratch/stefan/7787021/working/building/REAL300025241758 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/639 `/scratch/stefan/7787021/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241758.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241758 none CC(CCNC(=O)C1=CCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 5, 12, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 119, 136, 161, 172, 173, 173, 173, 201, 201, 201, 201, 201, 87, 119, 33, 86, 13, 1, 1, 1, 1, 1, 1, 1, 136, 136, 136, 136, 161, 161, 172, 172, 173, 201, 201, 201, 201, 201, 201, 201, 119, 119, 119, 33, 33, 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: 738 number of broken/clashed sets: 119 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241758 none CC(CCNC(=O)C1=CCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 5, 12, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 18, 16, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 26, 29, 29, 38, 38, 75, 121, 201, 201, 201, 201, 201, 26, 26, 26, 26, 19, 19, 16, 16, 8, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 75, 75, 201] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46]) total number of confs: 556 number of broken/clashed sets: 119 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241758 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241758 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241758/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241758 Building REAL300025241759 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241759' /scratch/stefan/7787021/working/building/REAL300025241759 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241759 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241759/0 /scratch/stefan/7787021/working/building/REAL300025241759 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/640 `/scratch/stefan/7787021/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1=COC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241759.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241759 none CC(CCNC(=O)CC1=COC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 1, 1, 12, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [56, 53, 56, 56, 56, 56, 56, 56, 125, 201, 201, 201, 201, 42, 53, 21, 42, 13, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 56, 56, 56, 56, 125, 125, 201, 201, 201, 53, 53, 53, 21, 21, 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: 643 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: REAL300025241759 none CC(CCNC(=O)CC1=COC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 1, 1, 12, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [15, 15, 15, 9, 9, 2, 9, 1, 1, 1, 1, 1, 1, 15, 17, 17, 23, 23, 56, 92, 201, 201, 201, 201, 201, 15, 15, 15, 15, 15, 15, 15, 15, 9, 2, 2, 1, 1, 1, 17, 17, 17, 56, 56, 201] 201 rigid atoms, others: [36, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 478 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241759 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241759 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241759/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241759 Building REAL300025241760 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241760' /scratch/stefan/7787021/working/building/REAL300025241760 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241760 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241760/0 /scratch/stefan/7787021/working/building/REAL300025241760 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/641 `/scratch/stefan/7787021/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=CO1) `REAL300025241760.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241760 none CC1=NC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 179, 156, 117, 100, 117, 62, 100, 27, 61, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 179, 179, 156, 156, 117, 117, 117, 117, 100, 100, 100, 27, 27, 1, 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]) total number of confs: 846 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241760 none CC1=NC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 8, 17, 17, 26, 26, 39, 39, 68, 106, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 6, 6, 9, 9, 17, 17, 17, 17, 26, 26, 26, 68, 68, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 43, 23, 24, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 523 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241760 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241760 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241760/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241760 Building REAL300025241761 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241761' /scratch/stefan/7787021/working/building/REAL300025241761 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241761 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241761/0 /scratch/stefan/7787021/working/building/REAL300025241761 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/642 `/scratch/stefan/7787021/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CCCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241761.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241761 none CC(CCNC(=O)C1=CCCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 73, 86, 93, 97, 97, 97, 97, 201, 201, 201, 201, 201, 201, 54, 73, 26, 54, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 93, 93, 97, 97, 97, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 73, 73, 73, 26, 26, 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: 547 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241761 none CC(CCNC(=O)C1=CCCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 13, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 19, 23, 23, 29, 29, 59, 94, 201, 201, 201, 201, 201, 19, 19, 19, 19, 14, 14, 12, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 59, 59, 201] 201 rigid atoms, others: [45, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 43, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 46, 47, 48, 49, 50, 51]) total number of confs: 495 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241761 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241761 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241761/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241761 Building REAL300025241762 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241762' /scratch/stefan/7787021/working/building/REAL300025241762 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241762 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241762/0 /scratch/stefan/7787021/working/building/REAL300025241762 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/643 `/scratch/stefan/7787021/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)[C@H](C)NC(N)=O)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241762.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241762 none CC(CCNC(=O)[C@H](C)NC(N)=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 8, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [99, 93, 99, 125, 146, 155, 155, 155, 201, 201, 201, 201, 201, 201, 78, 93, 32, 78, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 99, 125, 125, 146, 146, 155, 201, 201, 201, 201, 201, 201, 93, 93, 93, 32, 32, 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: 894 number of broken/clashed sets: 115 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241762 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241762 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241762/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241762 Building REAL300025241763 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241763' /scratch/stefan/7787021/working/building/REAL300025241763 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241763 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241763/0 /scratch/stefan/7787021/working/building/REAL300025241763 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/644 `/scratch/stefan/7787021/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1OCCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241763.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241763 none CC(CCNC(=O)CC1OCCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 54, 59, 74, 88, 96, 96, 96, 201, 201, 201, 201, 201, 201, 54, 54, 27, 54, 12, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 74, 74, 88, 88, 96, 201, 201, 201, 201, 201, 201, 201, 201, 201, 54, 54, 54, 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: 840 number of broken/clashed sets: 141 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241763 none CC(CCNC(=O)CC1OCCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 21, 12, 12, 4, 12, 1, 1, 1, 1, 1, 1, 1, 35, 36, 36, 38, 38, 72, 104, 201, 201, 201, 201, 201, 35, 35, 35, 35, 28, 28, 21, 21, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 72, 72, 201] 201 rigid atoms, others: [43, 37, 38, 7, 8, 9, 10, 11, 12, 13, 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, 44, 45, 46, 47, 48, 49]) total number of confs: 573 number of broken/clashed sets: 141 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241763 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241763 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241763/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241763 Building REAL300025241764 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241764' /scratch/stefan/7787021/working/building/REAL300025241764 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241764 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241764/0 /scratch/stefan/7787021/working/building/REAL300025241764 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/645 `/scratch/stefan/7787021/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=CO1) `REAL300025241764.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241764 none CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 151, 140, 125, 108, 125, 80, 108, 28, 80, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 153, 151, 151, 140, 140, 125, 125, 125, 125, 108, 108, 108, 28, 28, 1, 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]) total number of confs: 684 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241764 none CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 11, 13, 20, 20, 26, 26, 33, 33, 74, 120, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 5, 11, 11, 14, 14, 20, 20, 20, 20, 26, 26, 26, 74, 74, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 44, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 552 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241764 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241764 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241764/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241764 Building REAL300025241765 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241765' /scratch/stefan/7787021/working/building/REAL300025241765 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241765 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241765/0 /scratch/stefan/7787021/working/building/REAL300025241765 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/646 `/scratch/stefan/7787021/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)N(C)C=C1) `REAL300025241765.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241765 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 101, 101, 101, 100, 89, 72, 59, 72, 40, 59, 21, 40, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 101, 100, 100, 89, 89, 72, 72, 72, 72, 59, 59, 59, 21, 21, 1, 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]) total number of confs: 590 number of broken/clashed sets: 97 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241765 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 12, 14, 19, 19, 24, 24, 33, 33, 64, 101, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 7, 12, 12, 14, 14, 19, 19, 19, 19, 24, 24, 24, 64, 64, 201, 2, 2, 2, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 47, 48, 22, 23, 24, 25] set([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, 45, 46]) total number of confs: 523 number of broken/clashed sets: 97 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241765 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241765 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241765/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241765 Building REAL300025241766 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241766' /scratch/stefan/7787021/working/building/REAL300025241766 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241766 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241766/0 /scratch/stefan/7787021/working/building/REAL300025241766 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/647 `/scratch/stefan/7787021/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=CN=N1) `REAL300025241766.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241766 none CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 92, 92, 92, 92, 90, 87, 73, 87, 59, 73, 28, 59, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 92, 92, 92, 90, 90, 87, 87, 87, 87, 73, 73, 73, 28, 28, 1, 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]) total number of confs: 525 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241766 none CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 11, 10, 15, 15, 20, 20, 24, 24, 55, 92, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 5, 11, 11, 11, 11, 15, 15, 15, 15, 20, 20, 20, 55, 55, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 45, 23, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 486 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241766 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241766 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241766/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241766 Building REAL300025241767 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241767' /scratch/stefan/7787021/working/building/REAL300025241767 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241767 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241767/0 /scratch/stefan/7787021/working/building/REAL300025241767 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/648 `/scratch/stefan/7787021/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCN1C=CN=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241767.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241767 none CC(CCNC(=O)CCN1C=CN=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [56, 56, 56, 66, 86, 92, 92, 92, 186, 186, 201, 201, 201, 201, 47, 56, 26, 47, 13, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 66, 66, 86, 86, 92, 186, 186, 186, 186, 201, 201, 56, 56, 56, 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: 852 number of broken/clashed sets: 116 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241767 none CC(CCNC(=O)CCN1C=CN=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [31, 27, 23, 17, 17, 10, 17, 5, 1, 1, 1, 1, 1, 1, 31, 32, 32, 37, 37, 76, 113, 201, 201, 201, 201, 201, 31, 31, 31, 31, 27, 27, 23, 23, 17, 10, 10, 5, 5, 1, 1, 32, 32, 32, 76, 76, 201] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 578 number of broken/clashed sets: 116 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241767 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241767 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241767/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241767 Building REAL300025241768 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241768' /scratch/stefan/7787021/working/building/REAL300025241768 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241768 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241768/0 /scratch/stefan/7787021/working/building/REAL300025241768 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/649 `/scratch/stefan/7787021/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025241768.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241768 none CC(=O)N1CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 146, 201, 146, 146, 57, 57, 57, 57, 57, 39, 38, 39, 28, 38, 22, 28, 12, 1, 1, 1, 1, 1, 1, 1, 146, 201, 201, 201, 146, 146, 146, 57, 57, 57, 57, 57, 39, 39, 39, 39, 38, 38, 38, 22, 22, 1, 146, 146] 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]) total number of confs: 718 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: REAL300025241768 none CC(=O)N1CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 15, 15, 17, 17, 17, 17, 39, 39, 55, 78, 146, 146, 146, 146, 146, 1, 3, 3, 3, 1, 1, 1, 8, 15, 15, 15, 15, 17, 17, 17, 17, 17, 17, 17, 55, 55, 146, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 47, 48, 25, 29, 30, 31] set([0, 2, 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]) total number of confs: 411 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241768 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241768 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241768/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241768 Building REAL300025241769 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241769' /scratch/stefan/7787021/working/building/REAL300025241769 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241769 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241769/0 /scratch/stefan/7787021/working/building/REAL300025241769 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/650 `/scratch/stefan/7787021/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC(=O)N(C)O1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241769.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241769 none CC(CCNC(=O)C1=CC(=O)N(C)O1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 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: [123, 104, 123, 156, 173, 186, 186, 186, 201, 201, 201, 201, 201, 201, 76, 104, 30, 75, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 156, 156, 173, 173, 186, 201, 201, 201, 201, 104, 104, 104, 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: 790 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: REAL300025241769 none CC(CCNC(=O)C1=CC(=O)N(C)O1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 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: [19, 13, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 19, 24, 24, 36, 36, 69, 108, 201, 201, 201, 201, 201, 19, 19, 19, 19, 15, 15, 11, 11, 5, 1, 1, 1, 1, 24, 24, 24, 69, 69, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44]) total number of confs: 524 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241769 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241769 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241769/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241769 Building REAL300025241770 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241770' /scratch/stefan/7787021/working/building/REAL300025241770 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241770 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241770/0 /scratch/stefan/7787021/working/building/REAL300025241770 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/651 `/scratch/stefan/7787021/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241770.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241770 none CCC(C)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 60, 60, 60, 60, 60, 53, 52, 53, 52, 52, 28, 51, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 60, 60, 60, 60, 60, 53, 53, 53, 53, 52, 52, 52, 28, 28, 1] 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]) total number of confs: 788 number of broken/clashed sets: 154 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241770 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241770 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241770/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241770 Building REAL300025241771 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241771' /scratch/stefan/7787021/working/building/REAL300025241771 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241771 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241771/0 /scratch/stefan/7787021/working/building/REAL300025241771 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/652 `/scratch/stefan/7787021/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CCC1) `REAL300025241771.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241771 none COC1(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 184, 129, 129, 129, 122, 118, 104, 93, 104, 70, 93, 32, 69, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 184, 184, 129, 122, 122, 118, 118, 104, 104, 104, 104, 93, 93, 93, 32, 32, 1, 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]) total number of confs: 872 number of broken/clashed sets: 125 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241771 none COC1(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 20, 21, 25, 25, 27, 27, 29, 29, 61, 94, 201, 201, 201, 201, 201, 1, 1, 1, 5, 5, 5, 6, 6, 11, 20, 20, 22, 22, 25, 25, 25, 25, 27, 27, 27, 61, 61, 201, 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: 511 number of broken/clashed sets: 125 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241771 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241771 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241771/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241771 Building REAL300025241772 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241772' /scratch/stefan/7787021/working/building/REAL300025241772 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241772 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241772/0 /scratch/stefan/7787021/working/building/REAL300025241772 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/653 `/scratch/stefan/7787021/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCCOC1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241772.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241772 none CC(CCNC(=O)C1CCCOC1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 110, 123, 134, 146, 147, 147, 147, 201, 201, 201, 201, 201, 201, 81, 110, 30, 81, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 134, 134, 146, 146, 147, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 110, 110, 110, 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: 731 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: REAL300025241772 none CC(CCNC(=O)C1CCCOC1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 14, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 21, 25, 25, 32, 32, 68, 114, 201, 201, 201, 201, 201, 21, 21, 21, 21, 15, 15, 12, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 25, 25, 25, 68, 68, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 39, 12, 13, 11, 40, 41, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 533 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241772 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241772 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241772/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241772 Building REAL300025241773 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241773' /scratch/stefan/7787021/working/building/REAL300025241773 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241773 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241773/0 /scratch/stefan/7787021/working/building/REAL300025241773 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/654 `/scratch/stefan/7787021/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241773.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241773 none C#CCCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 155, 156, 55, 55, 55, 55, 55, 40, 39, 40, 28, 40, 22, 28, 11, 1, 1, 1, 1, 1, 1, 1, 201, 191, 191, 175, 175, 156, 156, 55, 55, 55, 55, 55, 40, 40, 40, 40, 40, 40, 40, 22, 22, 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: 973 number of broken/clashed sets: 83 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241773 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241773 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241773/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241773 Building REAL300025241774 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241774' /scratch/stefan/7787021/working/building/REAL300025241774 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241774 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241774/0 /scratch/stefan/7787021/working/building/REAL300025241774 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/655 `/scratch/stefan/7787021/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=C(Cl)OC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241774.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241774 none CC(CCNC(=O)C1=C(Cl)OC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 1, 1, 16, 12, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 56, 65, 71, 76, 77, 77, 77, 201, 201, 201, 201, 201, 42, 56, 21, 42, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 71, 71, 76, 76, 77, 201, 201, 56, 56, 56, 21, 21, 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: 467 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241774 none CC(CCNC(=O)C1=C(Cl)OC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 1, 1, 16, 12, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 23, 23, 29, 29, 56, 97, 201, 201, 201, 201, 201, 19, 19, 19, 19, 15, 15, 12, 12, 6, 1, 1, 23, 23, 23, 56, 56, 201] 201 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 493 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241774 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241774 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241774/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241774 Building REAL300025241775 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241775' /scratch/stefan/7787021/working/building/REAL300025241775 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241775 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241775/0 /scratch/stefan/7787021/working/building/REAL300025241775 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/656 `/scratch/stefan/7787021/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=NS1) `REAL300025241775.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241775 none CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 7] 0 hydrogens need 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, 167, 147, 115, 101, 115, 60, 101, 26, 60, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 167, 167, 147, 147, 115, 115, 115, 115, 101, 101, 101, 26, 26, 1] 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]) total number of confs: 814 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241775 none CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 8, 9, 16, 16, 25, 25, 38, 38, 67, 106, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 2, 8, 8, 9, 9, 16, 16, 16, 16, 25, 25, 25, 67, 67, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 514 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241775 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241775 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241775/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241775 Building REAL300025241776 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241776' /scratch/stefan/7787021/working/building/REAL300025241776 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241776 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241776/0 /scratch/stefan/7787021/working/building/REAL300025241776 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/657 `/scratch/stefan/7787021/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=CN=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241776.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241776 none CCN1C=CN=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 107, 107, 107, 107, 107, 107, 107, 107, 84, 82, 68, 57, 68, 37, 57, 22, 37, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 107, 107, 107, 84, 84, 82, 82, 68, 68, 68, 68, 57, 57, 57, 22, 22, 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: 983 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: REAL300025241776 none CCN1C=CN=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 2, 2, 2, 6, 7, 10, 10, 14, 14, 20, 20, 37, 58, 107, 107, 107, 107, 107, 3, 3, 3, 3, 3, 1, 1, 2, 6, 6, 7, 7, 10, 10, 10, 10, 14, 14, 14, 37, 37, 107] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 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, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 291 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241776 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241776 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241776/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241776 Building REAL300025241777 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241777' /scratch/stefan/7787021/working/building/REAL300025241777 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241777 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241777/0 /scratch/stefan/7787021/working/building/REAL300025241777 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/658 `/scratch/stefan/7787021/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241777.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241777 none CC(CCNC(=O)C1CCCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 84, 94, 97, 101, 101, 101, 101, 201, 201, 201, 201, 201, 201, 65, 84, 26, 64, 13, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 97, 97, 101, 101, 101, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 84, 84, 84, 26, 26, 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: 673 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241777 none CC(CCNC(=O)C1CCCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 13, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 19, 22, 22, 27, 27, 61, 99, 201, 201, 201, 201, 201, 19, 19, 19, 19, 14, 14, 12, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 61, 61, 201] 201 rigid atoms, others: [45, 35, 36, 5, 38, 7, 8, 9, 10, 39, 12, 13, 44, 11, 40, 43, 41, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 46, 47, 48, 49, 50, 51]) total number of confs: 497 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241777 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241777 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241777/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241777 Building REAL300025241778 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241778' /scratch/stefan/7787021/working/building/REAL300025241778 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241778 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241778/0 /scratch/stefan/7787021/working/building/REAL300025241778 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/659 `/scratch/stefan/7787021/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1=NC=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241778.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241778 none CC(CCNC(=O)CCC1=NC=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 56, 59, 75, 107, 147, 147, 147, 201, 201, 201, 201, 201, 201, 48, 56, 24, 47, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 75, 75, 107, 107, 147, 201, 201, 201, 201, 201, 201, 201, 56, 56, 56, 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: 923 number of broken/clashed sets: 98 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241778 none CC(CCNC(=O)CCC1=NC=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 16, 7, 7, 5, 7, 5, 1, 1, 1, 1, 1, 1, 26, 27, 27, 33, 33, 71, 107, 201, 201, 201, 201, 201, 26, 26, 26, 26, 20, 20, 16, 16, 7, 5, 5, 5, 5, 1, 1, 1, 27, 27, 27, 71, 71, 201] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46, 47]) total number of confs: 566 number of broken/clashed sets: 114 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241778 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241778 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241778/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241778 Building REAL300025241779 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241779' /scratch/stefan/7787021/working/building/REAL300025241779 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241779 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241779/0 /scratch/stefan/7787021/working/building/REAL300025241779 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/660 `/scratch/stefan/7787021/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCC(O)CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241779.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241779 none CC(CCNC(=O)C1CCC(O)CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 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: [85, 80, 85, 88, 92, 93, 93, 93, 201, 201, 201, 201, 201, 201, 64, 80, 26, 63, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 88, 88, 92, 92, 93, 201, 201, 201, 201, 201, 201, 603, 201, 201, 201, 201, 80, 80, 80, 26, 26, 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: 1272 number of broken/clashed sets: 276 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241779 none CC(CCNC(=O)C1CCC(O)CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 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: [24, 19, 16, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 24, 26, 26, 32, 32, 67, 114, 201, 201, 201, 201, 201, 24, 24, 24, 24, 19, 19, 16, 16, 8, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 26, 26, 26, 67, 67, 201] 603 rigid atoms, others: [45, 35, 36, 5, 38, 7, 8, 9, 10, 39, 12, 13, 44, 11, 40, 43, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 46, 47, 48, 49, 50, 51]) total number of confs: 524 number of broken/clashed sets: 276 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241779 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241779 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241779/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241779 Building REAL300025241780 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241780' /scratch/stefan/7787021/working/building/REAL300025241780 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241780 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241780/0 /scratch/stefan/7787021/working/building/REAL300025241780 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/661 `/scratch/stefan/7787021/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC(C)(C)O)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241780.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241780 none CC(CCNC(=O)CC(C)(C)O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [100, 92, 100, 125, 139, 147, 147, 147, 201, 201, 201, 201, 73, 92, 29, 72, 13, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 125, 125, 139, 139, 147, 201, 201, 201, 201, 201, 201, 201, 201, 603, 92, 92, 92, 29, 29, 1] 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]) total number of confs: 1456 number of broken/clashed sets: 316 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241780 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241780 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241780/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241780 Building REAL300025241781 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241781' /scratch/stefan/7787021/working/building/REAL300025241781 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241781 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241781/0 /scratch/stefan/7787021/working/building/REAL300025241781 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/662 `/scratch/stefan/7787021/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=N1) `REAL300025241781.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241781 none CC1=CC=NC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 201, 107, 107, 107, 106, 98, 78, 65, 78, 45, 65, 23, 45, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 200, 201, 107, 106, 106, 98, 98, 78, 78, 78, 78, 65, 65, 65, 23, 23, 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: 620 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241781 none CC1=CC=NC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 9, 11, 17, 17, 21, 21, 29, 29, 60, 100, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 5, 9, 9, 11, 11, 17, 17, 17, 17, 21, 21, 21, 60, 60, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 29, 30] set([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: 504 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241781 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241781 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241781/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241781 Building REAL300025241782 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241782' /scratch/stefan/7787021/working/building/REAL300025241782 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241782 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241782/0 /scratch/stefan/7787021/working/building/REAL300025241782 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/663 `/scratch/stefan/7787021/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)C1CC1) `REAL300025241782.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241782 none COC(C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)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.3', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 13, 15, 23, 23, 29, 29, 36, 36, 70, 109, 201, 201, 201, 201, 201, 1, 1, 1, 4, 4, 4, 4, 6, 13, 13, 16, 16, 23, 23, 23, 23, 29, 29, 29, 70, 70, 201, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 44, 45, 46, 47, 48, 22, 23, 24] set([0, 1, 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: 560 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: REAL300025241782 none COC(C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)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.3', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 150, 136, 113, 78, 66, 78, 47, 66, 26, 47, 13, 1, 1, 1, 1, 1, 1, 1, 150, 201, 201, 150, 150, 150, 150, 150, 136, 136, 113, 113, 78, 78, 78, 78, 66, 66, 66, 26, 26, 1, 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]) total number of confs: 865 number of broken/clashed sets: 126 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241782 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241782 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241782/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241782 Building REAL300025241783 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241783' /scratch/stefan/7787021/working/building/REAL300025241783 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241783 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241783/0 /scratch/stefan/7787021/working/building/REAL300025241783 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/664 `/scratch/stefan/7787021/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=CO1) `REAL300025241783.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241783 none CCC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 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, 176, 176, 150, 150, 150, 150, 140, 122, 108, 122, 83, 108, 32, 83, 13, 1, 1, 1, 1, 1, 1, 1, 176, 176, 176, 201, 201, 201, 201, 201, 150, 150, 150, 140, 140, 122, 122, 122, 122, 108, 108, 108, 32, 32, 1, 176, 176] 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]) total number of confs: 774 number of broken/clashed sets: 130 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241783 none CCC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 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, 3, 3, 3, 8, 8, 13, 13, 14, 14, 18, 18, 47, 78, 176, 176, 176, 176, 176, 1, 1, 1, 5, 5, 5, 5, 5, 3, 7, 7, 10, 10, 13, 13, 13, 13, 14, 14, 14, 47, 47, 176, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 46, 47, 23, 24, 25] set([0, 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: 428 number of broken/clashed sets: 130 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241783 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241783 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241783/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241783 Building REAL300025241784 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241784' /scratch/stefan/7787021/working/building/REAL300025241784 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241784 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241784/0 /scratch/stefan/7787021/working/building/REAL300025241784 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/665 `/scratch/stefan/7787021/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CN=NN1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241784.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241784 none CC(CCNC(=O)C1=CN=NN1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [120, 104, 120, 149, 169, 189, 189, 189, 201, 201, 201, 201, 201, 73, 104, 31, 73, 13, 1, 1, 1, 1, 1, 1, 1, 120, 120, 120, 120, 149, 149, 169, 169, 189, 201, 201, 201, 201, 104, 104, 104, 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: 794 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: REAL300025241784 none CC(CCNC(=O)C1=CN=NN1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 11, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 17, 25, 25, 35, 35, 68, 107, 201, 201, 201, 201, 201, 17, 17, 17, 17, 12, 12, 10, 10, 4, 1, 2, 2, 2, 25, 25, 25, 68, 68, 201] 201 rigid atoms, others: [34, 5, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 525 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241784 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241784 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241784/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241784 Building REAL300025241785 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241785' /scratch/stefan/7787021/working/building/REAL300025241785 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241785 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241785/0 /scratch/stefan/7787021/working/building/REAL300025241785 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/666 `/scratch/stefan/7787021/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241785.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241785 none CCCCC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 60, 176, 60, 60, 57, 57, 41, 40, 41, 30, 41, 21, 30, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 176, 176, 176, 176, 60, 57, 57, 57, 57, 41, 41, 41, 41, 41, 41, 41, 21, 21, 1] 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]) total number of confs: 869 number of broken/clashed sets: 83 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241785 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241785 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241785/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241785 Building REAL300025241786 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241786' /scratch/stefan/7787021/working/building/REAL300025241786 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241786 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241786/0 /scratch/stefan/7787021/working/building/REAL300025241786 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/667 `/scratch/stefan/7787021/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1OC(C)CC1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241786.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241786 none CC(CCNC(=O)C1OC(C)CC1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 117, 143, 176, 184, 196, 196, 196, 201, 201, 201, 201, 201, 201, 80, 117, 30, 80, 13, 1, 1, 1, 1, 1, 1, 1, 143, 143, 143, 143, 176, 176, 184, 184, 196, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 117, 117, 117, 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: 802 number of broken/clashed sets: 101 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241786 none CC(CCNC(=O)C1OC(C)CC1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 17, 23, 23, 31, 31, 64, 103, 201, 201, 201, 201, 201, 17, 17, 17, 17, 12, 12, 11, 11, 4, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 23, 23, 23, 64, 64, 201] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 40, 41, 42] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 518 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241786 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241786 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241786/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241786 Building REAL300025241787 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241787' /scratch/stefan/7787021/working/building/REAL300025241787 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241787 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241787/0 /scratch/stefan/7787021/working/building/REAL300025241787 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/668 `/scratch/stefan/7787021/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)[C@H]1C[C@@H]1C(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241787.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241787 none CC(CCNC(=O)[C@H]1C[C@@H]1C(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [84, 82, 84, 95, 122, 124, 124, 124, 201, 201, 201, 201, 201, 201, 201, 73, 82, 31, 72, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 95, 95, 122, 122, 124, 201, 201, 201, 82, 82, 82, 31, 31, 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: 748 number of broken/clashed sets: 134 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241787 none CC(CCNC(=O)[C@H]1C[C@@H]1C(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [20, 19, 14, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 6, 6, 20, 22, 22, 25, 25, 55, 92, 201, 201, 201, 201, 201, 20, 20, 20, 20, 19, 19, 14, 14, 9, 1, 1, 6, 22, 22, 22, 55, 55, 201] 201 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 494 number of broken/clashed sets: 134 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241787 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241787 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241787/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241787 Building REAL300025241788 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241788' /scratch/stefan/7787021/working/building/REAL300025241788 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241788 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241788/0 /scratch/stefan/7787021/working/building/REAL300025241788 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/669 `/scratch/stefan/7787021/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC(C)=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241788.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241788 none CC1=COC(C)=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 102, 102, 102, 101, 94, 87, 81, 87, 66, 81, 26, 66, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 102, 101, 101, 94, 94, 87, 87, 87, 87, 81, 81, 81, 26, 26, 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: 530 number of broken/clashed sets: 108 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241788 none CC1=COC(C)=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 201 conformations 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, 17, 19, 27, 27, 28, 28, 33, 33, 69, 107, 201, 201, 201, 201, 201, 2, 2, 2, 1, 2, 2, 2, 8, 17, 17, 20, 20, 27, 27, 27, 27, 28, 28, 28, 69, 69, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29] set([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, 45, 46, 47]) total number of confs: 540 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241788 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241788 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241788/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241788 Building REAL300025241789 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241789' /scratch/stefan/7787021/working/building/REAL300025241789 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241789 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241789/0 /scratch/stefan/7787021/working/building/REAL300025241789 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/670 `/scratch/stefan/7787021/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CC(C)(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241789.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241789 none CC(CCNC(=O)C1CC(C)(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 76, 81, 85, 89, 89, 89, 89, 201, 201, 201, 201, 201, 56, 76, 24, 56, 13, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 85, 85, 89, 89, 89, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 76, 76, 76, 24, 24, 1] 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]) total number of confs: 674 number of broken/clashed sets: 101 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241789 none CC(CCNC(=O)C1CC(C)(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 18, 15, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 26, 26, 31, 31, 66, 100, 201, 201, 201, 201, 201, 24, 24, 24, 24, 18, 18, 15, 15, 10, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 26, 26, 26, 66, 66, 201] 201 rigid atoms, others: [34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 44, 43] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50]) total number of confs: 529 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241789 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241789 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241789/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241789 Building REAL300025241790 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241790' /scratch/stefan/7787021/working/building/REAL300025241790 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241790 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241790/0 /scratch/stefan/7787021/working/building/REAL300025241790 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/671 `/scratch/stefan/7787021/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241790.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241790 none CC(C)[C@@H](O)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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, 7, 7, 4, 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, 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, 201, 179, 192, 192, 179, 179, 171, 141, 122, 102, 122, 67, 102, 31, 67, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 576, 179, 171, 171, 141, 141, 122, 122, 122, 122, 102, 102, 102, 31, 31, 1] 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]) total number of confs: 1464 number of broken/clashed sets: 372 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241790 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241790 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241790/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241790 Building REAL300025241791 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241791' /scratch/stefan/7787021/working/building/REAL300025241791 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241791 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241791/0 /scratch/stefan/7787021/working/building/REAL300025241791 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/672 `/scratch/stefan/7787021/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025241791.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241791 none CCOC1CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 93, 93, 67, 66, 67, 50, 67, 35, 50, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 98, 93, 93, 93, 93, 67, 67, 67, 67, 67, 67, 67, 35, 35, 1, 201, 201] 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]) total number of confs: 708 number of broken/clashed sets: 105 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241791 none CCOC1CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 8, 8, 8, 9, 9, 12, 12, 12, 12, 29, 29, 45, 78, 201, 201, 201, 201, 201, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 45, 45, 201, 1, 1] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 34, 50, 51, 25, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 443 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241791 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241791 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241791/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241791 Building REAL300025241792 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241792' /scratch/stefan/7787021/working/building/REAL300025241792 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241792 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241792/0 /scratch/stefan/7787021/working/building/REAL300025241792 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/673 `/scratch/stefan/7787021/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1(C)CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241792.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241792 none CC(CCNC(=O)CC1(C)CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 60, 63, 81, 94, 102, 102, 102, 178, 201, 201, 201, 201, 201, 50, 60, 25, 50, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 81, 81, 94, 94, 102, 178, 178, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 60, 60, 60, 25, 25, 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: 905 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: REAL300025241792 none CC(CCNC(=O)CC1(C)CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 12, 12, 4, 12, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 33, 33, 68, 102, 201, 201, 201, 201, 201, 27, 27, 27, 27, 22, 22, 20, 20, 12, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 68, 68, 201] 201 rigid atoms, others: [45, 43, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 41, 47, 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, 38, 39, 48, 49, 50, 51, 52, 53]) total number of confs: 544 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241792 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241792 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241792/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241792 Building REAL300025241793 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241793' /scratch/stefan/7787021/working/building/REAL300025241793 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241793 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241793/0 /scratch/stefan/7787021/working/building/REAL300025241793 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/674 `/scratch/stefan/7787021/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CN(C)N=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241793.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241793 none CC(CCNC(=O)C1=CN(C)N=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 8, 5, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [116, 102, 116, 151, 167, 201, 201, 201, 201, 201, 201, 201, 201, 66, 102, 28, 65, 13, 1, 1, 1, 1, 1, 1, 1, 116, 116, 116, 116, 151, 151, 167, 167, 201, 201, 201, 201, 201, 102, 102, 102, 28, 28, 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: 819 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: REAL300025241793 none CC(CCNC(=O)C1=CN(C)N=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 8, 5, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [15, 8, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 23, 23, 37, 37, 67, 109, 201, 201, 201, 201, 201, 15, 15, 15, 15, 8, 8, 6, 6, 1, 1, 2, 2, 2, 23, 23, 23, 67, 67, 201] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 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: 516 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241793 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241793 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241793/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241793 Building REAL300025241794 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241794' /scratch/stefan/7787021/working/building/REAL300025241794 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241794 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241794/0 /scratch/stefan/7787021/working/building/REAL300025241794 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/675 `/scratch/stefan/7787021/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)O1) `REAL300025241794.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241794 none CC1=NN=C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 74, 74, 48, 47, 48, 35, 48, 26, 35, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 86, 74, 74, 74, 74, 48, 48, 48, 48, 48, 48, 48, 26, 26, 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: 890 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: REAL300025241794 none CC1=NN=C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 11, 11, 11, 15, 15, 21, 21, 21, 21, 46, 46, 65, 100, 201, 201, 201, 201, 201, 1, 2, 2, 2, 3, 3, 11, 15, 15, 15, 15, 21, 21, 21, 21, 21, 21, 21, 65, 65, 201] 201 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, 44, 45]) total number of confs: 525 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241794 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241794 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241794/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241794 Building REAL300025241795 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241795' /scratch/stefan/7787021/working/building/REAL300025241795 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241795 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241795/0 /scratch/stefan/7787021/working/building/REAL300025241795 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/676 `/scratch/stefan/7787021/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=NN(C)C=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241795.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241795 none CC(CCNC(=O)C1=NN(C)C=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 8, 8, 5, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [94, 78, 94, 123, 136, 139, 139, 139, 201, 201, 201, 201, 201, 57, 78, 26, 56, 13, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 123, 123, 136, 136, 139, 201, 201, 201, 201, 78, 78, 78, 26, 26, 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: 702 number of broken/clashed sets: 97 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241795 none CC(CCNC(=O)C1=NN(C)C=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 8, 8, 5, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [15, 10, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 20, 20, 27, 27, 58, 97, 201, 201, 201, 201, 201, 15, 15, 15, 15, 10, 10, 6, 6, 2, 2, 2, 2, 1, 20, 20, 20, 58, 58, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 513 number of broken/clashed sets: 97 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241795 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241795 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241795/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241795 Building REAL300025241796 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241796' /scratch/stefan/7787021/working/building/REAL300025241796 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241796 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241796/0 /scratch/stefan/7787021/working/building/REAL300025241796 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/677 `/scratch/stefan/7787021/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241796.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241796 none CNC(=O)NCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 4, 7, 6, 4, 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, 7, 7, 7, 7] 0 hydrogens need 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, 185, 120, 120, 120, 107, 102, 78, 59, 78, 49, 60, 34, 49, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 185, 185, 185, 185, 120, 107, 107, 102, 102, 78, 78, 78, 78, 60, 60, 60, 34, 34, 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: 898 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241796 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241796 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241796/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241796 Building REAL300025241797 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241797' /scratch/stefan/7787021/working/building/REAL300025241797 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241797 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241797/0 /scratch/stefan/7787021/working/building/REAL300025241797 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/678 `/scratch/stefan/7787021/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=C(F)C=CS1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241797.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241797 none CC(CCNC(=O)C1=C(F)C=CS1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 1, 1, 15, 1, 1, 14, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 73, 86, 105, 113, 113, 113, 113, 201, 201, 201, 201, 201, 52, 73, 24, 52, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 105, 105, 113, 113, 113, 201, 201, 73, 73, 73, 24, 24, 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: 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: REAL300025241797 none CC(CCNC(=O)C1=C(F)C=CS1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 1, 1, 15, 1, 1, 14, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 11, 9, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 23, 23, 31, 31, 63, 102, 201, 201, 201, 201, 201, 17, 17, 17, 17, 11, 11, 9, 9, 7, 1, 1, 23, 23, 23, 63, 63, 201] 201 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 508 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241797 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241797 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241797/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241797 Building REAL300025241798 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241798' /scratch/stefan/7787021/working/building/REAL300025241798 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241798 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241798/0 /scratch/stefan/7787021/working/building/REAL300025241798 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/679 `/scratch/stefan/7787021/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=N1) `REAL300025241798.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241798 none CCN1N=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 111, 111, 111, 111, 111, 111, 111, 98, 98, 85, 61, 85, 49, 62, 32, 49, 13, 1, 1, 1, 1, 1, 1, 1, 111, 201, 201, 201, 201, 201, 111, 111, 98, 98, 98, 98, 85, 85, 85, 85, 62, 62, 62, 32, 32, 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: 1012 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: REAL300025241798 none CCN1N=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 11, 11, 22, 22, 36, 55, 111, 111, 111, 111, 111, 1, 6, 6, 6, 6, 6, 1, 1, 6, 6, 6, 6, 8, 8, 8, 8, 11, 11, 11, 36, 36, 111] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 25, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 299 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241798 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241798 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241798/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241798 Building REAL300025241799 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241799' /scratch/stefan/7787021/working/building/REAL300025241799 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241799 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241799/0 /scratch/stefan/7787021/working/building/REAL300025241799 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/680 `/scratch/stefan/7787021/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC(C)(C)C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241799.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241799 none CC(CCNC(=O)CC(C)(C)C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 65, 66, 89, 103, 122, 122, 122, 133, 154, 154, 154, 201, 201, 55, 65, 26, 55, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 89, 89, 103, 103, 122, 133, 133, 154, 154, 154, 154, 154, 154, 201, 201, 201, 201, 201, 65, 65, 65, 26, 26, 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: 869 number of broken/clashed sets: 139 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241799 none CC(CCNC(=O)CC(C)(C)C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 17, 15, 9, 9, 8, 9, 5, 1, 5, 5, 1, 1, 1, 21, 23, 23, 25, 25, 55, 96, 201, 201, 201, 201, 201, 21, 21, 21, 21, 17, 17, 15, 15, 9, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 23, 23, 23, 55, 55, 201] 201 rigid atoms, others: [11, 8, 44, 43, 12, 13, 46, 45, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 40, 41, 42, 48, 49, 50, 51, 52, 53]) total number of confs: 496 number of broken/clashed sets: 139 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241799 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241799 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241799/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241799 Building REAL300025241800 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241800' /scratch/stefan/7787021/working/building/REAL300025241800 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241800 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241800/0 /scratch/stefan/7787021/working/building/REAL300025241800 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/681 `/scratch/stefan/7787021/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=NC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241800.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241800 none CCN1N=NC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need 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, 140, 140, 140, 103, 103, 103, 102, 91, 85, 84, 85, 65, 84, 26, 65, 11, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 140, 103, 102, 102, 91, 91, 85, 85, 85, 85, 84, 84, 84, 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: 809 number of broken/clashed sets: 112 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241800 none CCN1N=NC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 4, 4, 4, 9, 12, 17, 17, 17, 17, 22, 22, 47, 72, 140, 140, 140, 140, 140, 4, 4, 4, 4, 4, 1, 4, 9, 9, 12, 12, 17, 17, 17, 17, 17, 17, 17, 47, 47, 140] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 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, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 371 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241800 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241800 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241800/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241800 Building REAL300025241801 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241801' /scratch/stefan/7787021/working/building/REAL300025241801 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241801 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241801/0 /scratch/stefan/7787021/working/building/REAL300025241801 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/682 `/scratch/stefan/7787021/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1) `REAL300025241801.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241801 none CC1=CSC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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: [201, 201, 201, 201, 192, 192, 192, 177, 154, 118, 102, 118, 67, 102, 24, 67, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 192, 177, 177, 154, 154, 118, 118, 118, 118, 102, 102, 102, 24, 24, 1, 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]) total number of confs: 798 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241801 none CC1=CSC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 1, 1, 5, 5, 5, 11, 12, 18, 18, 24, 24, 33, 33, 62, 99, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 5, 11, 11, 12, 12, 18, 18, 18, 18, 24, 24, 24, 62, 62, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 24, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 497 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241801 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241801 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241801/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241801 Building REAL300025241802 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241802' /scratch/stefan/7787021/working/building/REAL300025241802 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241802 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241802/0 /scratch/stefan/7787021/working/building/REAL300025241802 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/683 `/scratch/stefan/7787021/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CC1(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241802.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241802 none CC(CCNC(=O)C1CC1(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 5, 5, 5, 15, 15, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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] 0 hydrogens 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, 74, 93, 111, 112, 119, 119, 119, 201, 201, 201, 201, 51, 74, 26, 51, 12, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 111, 111, 112, 112, 119, 201, 201, 201, 74, 74, 74, 26, 26, 1] 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]) total number of confs: 745 number of broken/clashed sets: 117 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241802 none CC(CCNC(=O)C1CC1(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 5, 5, 5, 15, 15, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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] 0 hydrogens 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, 14, 7, 7, 1, 7, 1, 1, 1, 1, 1, 24, 32, 32, 47, 47, 83, 119, 201, 201, 201, 201, 201, 24, 24, 24, 24, 15, 15, 14, 14, 7, 1, 1, 1, 32, 32, 32, 83, 83, 201] 201 rigid atoms, others: [33, 34, 35, 5, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 591 number of broken/clashed sets: 117 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241802 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241802 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241802/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241802 Building REAL300025241803 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241803' /scratch/stefan/7787021/working/building/REAL300025241803 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241803 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241803/0 /scratch/stefan/7787021/working/building/REAL300025241803 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/684 `/scratch/stefan/7787021/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)=CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241803.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241803 none CCC(C)=CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 125, 125, 125, 91, 91, 91, 85, 78, 69, 65, 69, 48, 65, 24, 47, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 125, 125, 125, 125, 91, 85, 85, 78, 78, 69, 69, 69, 69, 65, 65, 65, 24, 24, 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: 936 number of broken/clashed sets: 131 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241803 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241803 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241803/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241803 Building REAL300025241804 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241804' /scratch/stefan/7787021/working/building/REAL300025241804 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241804 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241804/0 /scratch/stefan/7787021/working/building/REAL300025241804 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/685 `/scratch/stefan/7787021/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241804.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241804 none CC1=CN=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 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, 7] 0 hydrogens need 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, 139, 201, 201, 102, 102, 102, 101, 96, 93, 83, 93, 64, 83, 29, 64, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 102, 101, 101, 96, 96, 93, 93, 93, 93, 83, 83, 83, 29, 29, 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: 714 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241804 none CC1=CN=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations 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, 17, 18, 24, 24, 27, 27, 31, 31, 67, 102, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 10, 17, 17, 19, 19, 24, 24, 24, 24, 27, 27, 27, 67, 67, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 529 number of broken/clashed sets: 113 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241804 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241804 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241804/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241804 Building REAL300025241805 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241805' /scratch/stefan/7787021/working/building/REAL300025241805 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241805 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241805/0 /scratch/stefan/7787021/working/building/REAL300025241805 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/686 `/scratch/stefan/7787021/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C#CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241805.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241805 none CC(C)C#CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 191, 169, 131, 115, 131, 71, 115, 27, 70, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 191, 191, 169, 169, 131, 131, 131, 131, 115, 115, 115, 27, 27, 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: 810 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241805 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241805 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241805/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241805 Building REAL300025241806 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241806' /scratch/stefan/7787021/working/building/REAL300025241806 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241806 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241806/0 /scratch/stefan/7787021/working/building/REAL300025241806 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/687 `/scratch/stefan/7787021/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=CS1) `REAL300025241806.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241806 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 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, 7, 7, 7] 0 hydrogens need 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, 94, 88, 83, 77, 83, 58, 77, 23, 57, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 94, 94, 94, 88, 88, 83, 83, 83, 83, 77, 77, 77, 23, 23, 1, 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]) total number of confs: 524 number of broken/clashed sets: 111 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241806 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 18, 25, 25, 27, 27, 34, 34, 69, 113, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 8, 15, 15, 19, 19, 25, 25, 25, 25, 27, 27, 27, 69, 69, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 43, 44, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 549 number of broken/clashed sets: 111 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241806 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241806 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241806/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241806 Building REAL300025241807 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241807' /scratch/stefan/7787021/working/building/REAL300025241807 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241807 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241807/0 /scratch/stefan/7787021/working/building/REAL300025241807 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/688 `/scratch/stefan/7787021/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1(O)CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241807.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241807 none CC(CCNC(=O)CC1(O)CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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: [106, 99, 106, 131, 146, 147, 147, 147, 200, 201, 201, 201, 201, 83, 99, 30, 82, 12, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 106, 131, 131, 146, 146, 147, 200, 200, 603, 201, 201, 201, 201, 201, 201, 99, 99, 99, 30, 30, 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: 1470 number of broken/clashed sets: 342 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241807 none CC(CCNC(=O)CC1(O)CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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: [25, 19, 18, 11, 11, 5, 11, 1, 1, 1, 1, 1, 1, 25, 29, 29, 35, 35, 76, 125, 201, 201, 201, 201, 201, 25, 25, 25, 25, 21, 21, 18, 18, 11, 5, 5, 6, 1, 1, 1, 1, 1, 1, 29, 29, 29, 76, 76, 201] 603 rigid atoms, others: [37, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 564 number of broken/clashed sets: 342 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241807 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241807 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241807/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241807 Building REAL300025241808 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241808' /scratch/stefan/7787021/working/building/REAL300025241808 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241808 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241808/0 /scratch/stefan/7787021/working/building/REAL300025241808 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/689 `/scratch/stefan/7787021/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CNN=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241808.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241808 none CC1=CNN=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [201, 201, 201, 201, 201, 201, 201, 201, 177, 153, 122, 107, 122, 68, 107, 28, 68, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 177, 177, 153, 153, 122, 122, 122, 122, 107, 107, 107, 28, 28, 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: 841 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241808 none CC1=CNN=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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, 1, 1, 1, 1, 1, 1, 7, 9, 18, 18, 32, 32, 42, 42, 72, 111, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 7, 7, 10, 10, 18, 18, 18, 18, 32, 32, 32, 72, 72, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 540 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241808 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241808 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241808/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241808 Building REAL300025241809 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241809' /scratch/stefan/7787021/working/building/REAL300025241809 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241809 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241809/0 /scratch/stefan/7787021/working/building/REAL300025241809 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/690 `/scratch/stefan/7787021/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)=C1CCC1) `REAL300025241809.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241809 none CC(C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 7, 7, 7, 15, 18, 22, 22, 25, 25, 32, 32, 69, 110, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 7, 15, 15, 18, 18, 22, 22, 22, 22, 25, 25, 25, 69, 69, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 43, 44, 45, 46, 47, 48, 21, 22, 23, 24] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 533 number of broken/clashed sets: 101 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241809 none CC(C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 124, 117, 105, 96, 105, 74, 96, 28, 74, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 124, 124, 124, 117, 117, 105, 105, 105, 105, 96, 96, 96, 28, 28, 1, 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]) total number of confs: 731 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241809 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241809 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241809/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241809 Building REAL300025241810 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241810' /scratch/stefan/7787021/working/building/REAL300025241810 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241810 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241810/0 /scratch/stefan/7787021/working/building/REAL300025241810 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/691 `/scratch/stefan/7787021/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C#CC1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241810.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241810 none CC(CCNC(=O)C#CC1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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, 7] 0 hydrogens 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, 113, 129, 166, 191, 201, 201, 201, 201, 201, 201, 201, 70, 113, 28, 70, 13, 1, 1, 1, 1, 1, 1, 1, 129, 129, 129, 129, 166, 166, 191, 191, 201, 201, 201, 201, 201, 201, 113, 113, 113, 28, 28, 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: 824 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: REAL300025241810 none CC(CCNC(=O)C#CC1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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, 7] 0 hydrogens 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, 9, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 23, 23, 38, 38, 71, 106, 201, 201, 201, 201, 201, 17, 17, 17, 17, 10, 10, 7, 7, 1, 1, 1, 1, 1, 1, 23, 23, 23, 71, 71, 201] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 36, 37] set([0, 1, 2, 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]) total number of confs: 523 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241810 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241810 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241810/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241810 Building REAL300025241811 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241811' /scratch/stefan/7787021/working/building/REAL300025241811 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241811 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241811/0 /scratch/stefan/7787021/working/building/REAL300025241811 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/692 `/scratch/stefan/7787021/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C#CC(C)(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241811.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241811 none CC(CCNC(=O)C#CC(C)(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [134, 117, 134, 172, 191, 201, 201, 201, 201, 201, 201, 201, 201, 72, 117, 27, 71, 13, 1, 1, 1, 1, 1, 1, 1, 134, 134, 134, 134, 172, 172, 191, 191, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 117, 117, 117, 27, 27, 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: 803 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241811 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241811 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241811/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241811 Building REAL300025241812 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241812' /scratch/stefan/7787021/working/building/REAL300025241812 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241812 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241812/0 /scratch/stefan/7787021/working/building/REAL300025241812 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/693 `/scratch/stefan/7787021/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)N1) `REAL300025241812.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241812 none CC1=NN=C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 79, 79, 53, 52, 53, 37, 53, 27, 37, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 107, 79, 79, 79, 79, 53, 53, 53, 53, 53, 53, 53, 27, 27, 1, 201] 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]) total number of confs: 934 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: REAL300025241812 none CC1=NN=C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 10, 10, 10, 12, 12, 19, 19, 19, 19, 42, 42, 59, 92, 201, 201, 201, 201, 201, 1, 2, 2, 2, 5, 5, 10, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 59, 59, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 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, 44, 45]) total number of confs: 507 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241812 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241812/1 /scratch/stefan/7787021/working/building/REAL300025241812 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/694 `/scratch/stefan/7787021/working/3D/694' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=NN1) `REAL300025241812.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241812/1/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: REAL300025241812 none CC1=NC(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 139, 53, 53, 53, 53, 51, 47, 47, 47, 34, 47, 29, 34, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 139, 139, 53, 53, 53, 51, 51, 47, 47, 47, 47, 47, 47, 47, 29, 29, 1, 201] 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]) total number of confs: 682 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241812 none CC1=NC(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 4, 15, 15, 15, 18, 18, 20, 20, 20, 20, 46, 46, 62, 97, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 4, 4, 15, 18, 18, 18, 18, 20, 20, 20, 20, 20, 20, 20, 62, 62, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 46, 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, 44, 45]) total number of confs: 499 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241812 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241812 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241812/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241812/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241812 Building REAL300025241813 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241813' /scratch/stefan/7787021/working/building/REAL300025241813 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241813 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241813/0 /scratch/stefan/7787021/working/building/REAL300025241813 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/695 `/scratch/stefan/7787021/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)N=N1) `REAL300025241813.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241813 none CC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 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, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 201, 201, 201, 201, 142, 140, 109, 74, 109, 61, 74, 39, 61, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 142, 142, 140, 140, 109, 109, 109, 109, 74, 74, 74, 39, 39, 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: 861 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: REAL300025241813 none CC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 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, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 1, 3, 3, 3, 12, 14, 21, 21, 36, 36, 54, 54, 72, 112, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 3, 12, 12, 14, 14, 21, 21, 21, 21, 36, 36, 36, 72, 72, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 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: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241813 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241813 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241813/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241813 Building REAL300025241814 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241814' /scratch/stefan/7787021/working/building/REAL300025241814 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241814 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241814/0 /scratch/stefan/7787021/working/building/REAL300025241814 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/696 `/scratch/stefan/7787021/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)[C@@H]1C[C@H]1[N+](=O)[O-])N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241814.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241814 none CC(CCNC(=O)[C@@H]1C[C@H]1[N+](=O)[O-])N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 5, 7, 5, 5, 7, 8, 11, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 7, 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: [100, 94, 100, 112, 137, 139, 139, 139, 201, 201, 201, 201, 201, 201, 201, 78, 94, 28, 78, 13, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 112, 112, 137, 137, 139, 201, 201, 94, 94, 94, 28, 28, 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: 768 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: REAL300025241814 none CC(CCNC(=O)[C@@H]1C[C@H]1[N+](=O)[O-])N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 5, 7, 5, 5, 7, 8, 11, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 7, 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: [19, 17, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 6, 6, 19, 21, 21, 26, 26, 65, 109, 201, 201, 201, 201, 201, 19, 19, 19, 19, 17, 17, 12, 12, 8, 1, 1, 21, 21, 21, 65, 65, 201] 201 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 533 number of broken/clashed sets: 126 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241814 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241814 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241814/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241814 Building REAL300025241815 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241815' /scratch/stefan/7787021/working/building/REAL300025241815 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241815 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241815/0 /scratch/stefan/7787021/working/building/REAL300025241815 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/697 `/scratch/stefan/7787021/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN(C)N=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241815.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241815 none CC1=CN(C)N=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 201, 178, 153, 116, 99, 116, 61, 99, 27, 61, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 178, 178, 153, 153, 116, 116, 116, 116, 99, 99, 99, 27, 27, 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: 863 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241815 none CC1=CN(C)N=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 201 conformations 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, 2, 2, 2, 8, 10, 18, 18, 28, 28, 38, 38, 68, 109, 201, 201, 201, 201, 201, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 11, 11, 18, 18, 18, 18, 28, 28, 28, 68, 68, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29] set([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, 45, 46, 47]) total number of confs: 533 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241815 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241815 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241815/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241815 Building REAL300025241816 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241816' /scratch/stefan/7787021/working/building/REAL300025241816 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241816 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241816/0 /scratch/stefan/7787021/working/building/REAL300025241816 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/698 `/scratch/stefan/7787021/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCCC(F)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241816.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241816 none CC(CCNC(=O)C1CCCC(F)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 15, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7] 0 hydrogens 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, 93, 99, 102, 107, 108, 108, 108, 201, 201, 201, 201, 201, 201, 74, 93, 28, 74, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 99, 102, 102, 107, 107, 108, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 93, 93, 93, 28, 28, 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: 692 number of broken/clashed sets: 98 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241816 none CC(CCNC(=O)C1CCCC(F)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 15, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7] 0 hydrogens 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, 18, 16, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 25, 26, 26, 32, 32, 71, 120, 201, 201, 201, 201, 201, 25, 25, 25, 25, 19, 19, 16, 16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 71, 71, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 39, 12, 13, 44, 11, 40, 43, 41, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49, 50]) total number of confs: 539 number of broken/clashed sets: 98 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241816 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241816 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241816/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241816 Building REAL300025241817 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241817' /scratch/stefan/7787021/working/building/REAL300025241817 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241817 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241817/0 /scratch/stefan/7787021/working/building/REAL300025241817 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/699 `/scratch/stefan/7787021/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1=NN(C)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241817.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241817 none CC(CCNC(=O)CC1=NN(C)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 1, 8, 8, 5, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [48, 43, 48, 70, 87, 94, 94, 94, 201, 201, 201, 201, 201, 201, 43, 43, 23, 43, 13, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 70, 70, 87, 87, 94, 201, 201, 201, 201, 201, 201, 201, 43, 43, 43, 23, 23, 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: 835 number of broken/clashed sets: 139 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241817 none CC(CCNC(=O)CC1=NN(C)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 1, 8, 8, 5, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [38, 28, 21, 11, 11, 5, 11, 1, 1, 1, 1, 1, 1, 1, 38, 41, 41, 43, 43, 75, 109, 201, 201, 201, 201, 201, 38, 38, 38, 38, 28, 28, 21, 21, 11, 5, 5, 2, 2, 2, 1, 1, 41, 41, 41, 75, 75, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 40, 41] 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, 38, 39, 42, 43, 44, 45, 46, 47]) total number of confs: 588 number of broken/clashed sets: 139 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241817 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241817 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241817/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241817 Building REAL300025241818 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241818' /scratch/stefan/7787021/working/building/REAL300025241818 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241818 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241818/0 /scratch/stefan/7787021/working/building/REAL300025241818 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/700 `/scratch/stefan/7787021/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CC1) `REAL300025241818.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241818 none COCC1(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 155, 69, 69, 69, 65, 65, 44, 42, 44, 31, 42, 21, 31, 12, 1, 1, 1, 1, 1, 1, 1, 183, 183, 201, 201, 201, 201, 201, 155, 155, 69, 65, 65, 65, 65, 44, 44, 44, 44, 42, 42, 42, 21, 21, 1, 183, 183, 183, 183] 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: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241818 none COCC1(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 12, 12, 12, 14, 14, 17, 17, 18, 18, 43, 43, 56, 90, 183, 183, 183, 183, 183, 1, 1, 5, 5, 5, 4, 4, 5, 5, 12, 14, 14, 14, 14, 17, 17, 17, 17, 18, 18, 18, 56, 56, 183, 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: 457 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241818 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241818 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241818/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241818 Building REAL300025241819 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241819' /scratch/stefan/7787021/working/building/REAL300025241819 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241819 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241819/0 /scratch/stefan/7787021/working/building/REAL300025241819 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/701 `/scratch/stefan/7787021/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C)=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)S1) `REAL300025241819.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241819 none CC1=NC(C)=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)S1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 110, 110, 110, 110, 102, 91, 80, 91, 59, 80, 25, 59, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 110, 110, 110, 102, 102, 91, 91, 91, 91, 80, 80, 80, 25, 25, 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: 89 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241819 none CC1=NC(C)=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)S1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 201 conformations 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, 6, 6, 8, 11, 17, 17, 21, 21, 31, 31, 65, 103, 201, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 6, 8, 8, 11, 11, 17, 17, 17, 17, 21, 21, 21, 65, 65, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25] set([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, 44, 45, 46]) total number of confs: 521 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241819 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241819 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241819/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241819 Building REAL300025241820 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241820' /scratch/stefan/7787021/working/building/REAL300025241820 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241820 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241820/0 /scratch/stefan/7787021/working/building/REAL300025241820 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/702 `/scratch/stefan/7787021/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCNC(N)=O)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241820.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241820 none CC(CCNC(=O)CCNC(N)=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 43, 66, 77, 84, 84, 84, 186, 192, 192, 192, 201, 39, 41, 18, 38, 12, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 66, 66, 77, 77, 84, 186, 186, 192, 192, 201, 201, 201, 41, 41, 41, 18, 18, 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: 919 number of broken/clashed sets: 131 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241820 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241820 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241820/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241820 Building REAL300025241821 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241821' /scratch/stefan/7787021/working/building/REAL300025241821 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241821 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241821/0 /scratch/stefan/7787021/working/building/REAL300025241821 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/703 `/scratch/stefan/7787021/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CN1C(=O)CCC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241821.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241821 none CC(CCNC(=O)CN1C(=O)CCC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [109, 98, 109, 119, 119, 123, 123, 123, 201, 201, 201, 201, 201, 201, 201, 80, 98, 30, 80, 13, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 109, 119, 119, 119, 119, 123, 201, 201, 201, 201, 201, 201, 98, 98, 98, 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: 808 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: REAL300025241821 none CC(CCNC(=O)CN1C(=O)CCC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [19, 15, 17, 11, 11, 4, 11, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 23, 23, 60, 100, 201, 201, 201, 201, 201, 19, 19, 19, 19, 17, 17, 17, 17, 11, 4, 4, 1, 1, 1, 1, 19, 19, 19, 60, 60, 201] 201 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47]) total number of confs: 505 number of broken/clashed sets: 109 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241821 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241821 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241821/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241821 Building REAL300025241822 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241822' /scratch/stefan/7787021/working/building/REAL300025241822 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241822 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241822/0 /scratch/stefan/7787021/working/building/REAL300025241822 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/704 `/scratch/stefan/7787021/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241822.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241822 none CC1=CC=CC=C1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 152, 201, 201, 152, 41, 41, 41, 41, 41, 33, 33, 33, 23, 33, 18, 23, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 152, 201, 201, 152, 152, 41, 41, 41, 41, 41, 33, 33, 33, 33, 33, 33, 33, 18, 18, 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: 829 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241822 none CC1=CC=CC=C1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 16, 16, 16, 22, 23, 23, 23, 23, 23, 50, 50, 64, 102, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 5, 5, 16, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23, 23, 64, 64, 201] 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, 49, 50]) total number of confs: 506 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241822 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241822 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241822/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241822 Building REAL300025241823 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241823' /scratch/stefan/7787021/working/building/REAL300025241823 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241823 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241823/0 /scratch/stefan/7787021/working/building/REAL300025241823 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/705 `/scratch/stefan/7787021/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1=CC=CS1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241823.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241823 none CC(CCNC(=O)CCC1=CC=CS1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 14, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [37, 37, 37, 40, 44, 46, 46, 46, 172, 184, 201, 201, 201, 201, 37, 37, 22, 36, 13, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 40, 40, 44, 44, 46, 172, 172, 184, 184, 201, 201, 201, 37, 37, 37, 22, 22, 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: 743 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: REAL300025241823 none CC(CCNC(=O)CCC1=CC=CS1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 14, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [41, 39, 30, 21, 21, 5, 21, 3, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 79, 119, 201, 201, 201, 201, 201, 41, 41, 41, 41, 39, 39, 30, 30, 21, 5, 5, 3, 3, 1, 1, 1, 41, 41, 41, 79, 79, 201] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46, 47]) total number of confs: 585 number of broken/clashed sets: 146 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241823 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241823 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241823/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241823 Building REAL300025241824 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241824' /scratch/stefan/7787021/working/building/REAL300025241824 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241824 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241824/0 /scratch/stefan/7787021/working/building/REAL300025241824 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/706 `/scratch/stefan/7787021/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CN1C=CC=CC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241824.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241824 none CC(CCNC(=O)CN1C=CC=CC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [86, 80, 86, 114, 133, 156, 156, 156, 194, 201, 201, 201, 201, 201, 201, 70, 80, 29, 70, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 114, 114, 133, 133, 156, 194, 194, 201, 201, 201, 201, 80, 80, 80, 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: 826 number of broken/clashed sets: 122 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241824 none CC(CCNC(=O)CN1C=CC=CC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 27, 22, 10, 10, 2, 10, 1, 1, 1, 1, 1, 1, 1, 1, 29, 30, 30, 34, 34, 65, 105, 201, 201, 201, 201, 201, 29, 29, 29, 29, 27, 27, 22, 22, 10, 2, 2, 1, 1, 1, 1, 30, 30, 30, 65, 65, 201] 201 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47]) total number of confs: 520 number of broken/clashed sets: 122 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241824 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241824 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241824/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241824 Building REAL300025241825 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241825' /scratch/stefan/7787021/working/building/REAL300025241825 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241825 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241825/0 /scratch/stefan/7787021/working/building/REAL300025241825 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/707 `/scratch/stefan/7787021/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C(C)=NO1) `REAL300025241825.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241825 none CCC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C(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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 154, 154, 90, 90, 90, 90, 90, 90, 90, 90, 75, 90, 27, 75, 13, 1, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 201, 201, 201, 201, 201, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 27, 27, 1, 154, 154, 154] 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]) total number of confs: 676 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241825 none CCC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C(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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 32, 58, 154, 154, 154, 154, 154, 1, 1, 1, 1, 5, 5, 5, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 32, 32, 154, 2, 2, 2] 201 rigid atoms, others: [1, 2, 3, 4, 23, 24, 25, 26] set([0, 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, 48, 49]) total number of confs: 331 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241825 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241825 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241825/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241825 Building REAL300025241826 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241826' /scratch/stefan/7787021/working/building/REAL300025241826 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241826 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241826/0 /scratch/stefan/7787021/working/building/REAL300025241826 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/708 `/scratch/stefan/7787021/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C)=C1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241826.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241826 none CC1=NOC(C)=C1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 12, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 115, 48, 48, 48, 48, 48, 47, 47, 47, 39, 47, 20, 38, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 115, 115, 48, 48, 48, 48, 48, 47, 47, 47, 47, 47, 47, 47, 20, 20, 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: 629 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: REAL300025241826 none CC1=NOC(C)=C1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 12, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 2, 11, 11, 11, 12, 12, 13, 13, 13, 13, 19, 19, 53, 89, 201, 201, 201, 201, 201, 2, 2, 2, 2, 2, 2, 2, 2, 11, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 53, 53, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 467 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241826 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241826 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241826/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241826 Building REAL300025241827 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241827' /scratch/stefan/7787021/working/building/REAL300025241827 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241827 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241827/0 /scratch/stefan/7787021/working/building/REAL300025241827 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/709 `/scratch/stefan/7787021/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C)=C1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241827.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241827 none CC1=NNC(C)=C1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 94, 94, 94, 93, 93, 84, 77, 84, 60, 77, 28, 59, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 94, 93, 93, 93, 93, 84, 84, 84, 84, 77, 77, 77, 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: 819 number of broken/clashed sets: 104 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241827 none CC1=NNC(C)=C1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 2, 13, 13, 13, 17, 18, 21, 21, 21, 21, 23, 23, 52, 92, 201, 201, 201, 201, 201, 2, 2, 2, 1, 2, 2, 2, 2, 2, 13, 17, 17, 18, 18, 21, 21, 21, 21, 21, 21, 21, 52, 52, 201] 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, 49, 50]) total number of confs: 469 number of broken/clashed sets: 135 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241827 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241827 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241827/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241827 Building REAL300025241828 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241828' /scratch/stefan/7787021/working/building/REAL300025241828 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241828 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241828/0 /scratch/stefan/7787021/working/building/REAL300025241828 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/710 `/scratch/stefan/7787021/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC(C)=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241828.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241828 none CCC1=NOC(C)=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 174, 174, 174, 174, 174, 174, 64, 64, 64, 62, 58, 58, 58, 58, 49, 58, 23, 49, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 174, 174, 174, 64, 62, 62, 58, 58, 58, 58, 58, 58, 58, 58, 58, 23, 23, 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: 539 number of broken/clashed sets: 119 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241828 none CCC1=NOC(C)=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 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, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 12, 15, 15, 15, 15, 15, 18, 18, 44, 75, 174, 174, 174, 174, 174, 6, 6, 6, 5, 5, 2, 2, 2, 8, 12, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 44, 44, 174] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 418 number of broken/clashed sets: 119 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241828 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241828 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241828/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241828 Building REAL300025241829 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241829' /scratch/stefan/7787021/working/building/REAL300025241829 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241829 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241829/0 /scratch/stefan/7787021/working/building/REAL300025241829 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/711 `/scratch/stefan/7787021/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1CCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241829.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241829 none CC(CCNC(=O)CCC1CCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 49, 49, 49, 49, 139, 150, 201, 201, 201, 201, 201, 49, 49, 26, 49, 13, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 49, 139, 139, 165, 165, 201, 201, 201, 201, 201, 201, 201, 201, 201, 49, 49, 49, 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: 893 number of broken/clashed sets: 158 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241829 none CC(CCNC(=O)CCC1CCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 9, 27, 5, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 76, 124, 201, 201, 201, 201, 201, 31, 31, 31, 31, 31, 31, 27, 27, 27, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 76, 76, 201] 201 rigid atoms, others: [45, 43, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 46, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 551 number of broken/clashed sets: 158 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241829 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241829 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241829/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241829 Building REAL300025241830 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241830' /scratch/stefan/7787021/working/building/REAL300025241830 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241830 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241830/0 /scratch/stefan/7787021/working/building/REAL300025241830 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/712 `/scratch/stefan/7787021/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCC(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241830.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241830 none CC(CCNC(=O)C1CCC(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 83, 94, 102, 106, 106, 106, 106, 201, 201, 201, 201, 201, 62, 83, 25, 62, 13, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 102, 102, 106, 106, 106, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 83, 83, 83, 25, 25, 1] 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]) total number of confs: 687 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241830 none CC(CCNC(=O)C1CCC(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 16, 15, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 25, 25, 31, 31, 64, 108, 201, 201, 201, 201, 201, 21, 21, 21, 21, 17, 17, 15, 15, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 25, 25, 25, 64, 64, 201] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 44, 43, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 45, 46, 47, 48, 49, 50]) total number of confs: 522 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241830 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241830 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241830/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241830 Building REAL300025241831 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241831' /scratch/stefan/7787021/working/building/REAL300025241831 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241831 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241831/0 /scratch/stefan/7787021/working/building/REAL300025241831 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/713 `/scratch/stefan/7787021/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NOC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1) `REAL300025241831.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241831 none CC(C)C1=NOC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 184, 201, 184, 184, 184, 183, 183, 183, 143, 142, 116, 79, 116, 62, 79, 38, 62, 13, 1, 1, 1, 1, 1, 1, 1, 184, 201, 201, 201, 201, 201, 201, 201, 183, 143, 143, 142, 142, 116, 116, 116, 116, 79, 79, 79, 38, 38, 1, 184] 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, 49]) total number of confs: 902 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: REAL300025241831 none CC(C)C1=NOC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 4, 4, 3, 10, 11, 15, 15, 20, 20, 38, 38, 53, 85, 184, 184, 184, 184, 184, 1, 5, 5, 5, 5, 5, 5, 5, 4, 10, 10, 11, 11, 15, 15, 15, 15, 20, 20, 20, 53, 53, 184, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 49, 26] set([0, 2, 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, 48]) total number of confs: 449 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241831 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241831 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241831/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241831 Building REAL300025241832 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241832' /scratch/stefan/7787021/working/building/REAL300025241832 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241832 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241832/0 /scratch/stefan/7787021/working/building/REAL300025241832 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/714 `/scratch/stefan/7787021/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=N1) `REAL300025241832.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241832 none CCN1C=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 111, 111, 111, 111, 111, 111, 111, 97, 97, 84, 61, 84, 48, 62, 32, 48, 13, 1, 1, 1, 1, 1, 1, 1, 111, 201, 201, 201, 201, 201, 111, 111, 111, 97, 97, 97, 97, 84, 84, 84, 84, 62, 62, 62, 32, 32, 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: 1015 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: REAL300025241832 none CCN1C=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 6, 6, 8, 8, 12, 12, 25, 25, 37, 58, 111, 111, 111, 111, 111, 1, 5, 5, 5, 5, 5, 1, 1, 2, 6, 6, 6, 6, 8, 8, 8, 8, 12, 12, 12, 37, 37, 111] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 293 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241832 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241832 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241832/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241832 Building REAL300025241833 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241833' /scratch/stefan/7787021/working/building/REAL300025241833 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241833 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241833/0 /scratch/stefan/7787021/working/building/REAL300025241833 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/715 `/scratch/stefan/7787021/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCCCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241833.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241833 none CC(C)CCCCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 172, 201, 172, 150, 48, 48, 48, 48, 48, 47, 47, 47, 40, 47, 25, 40, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 150, 150, 48, 48, 48, 48, 48, 47, 47, 47, 47, 47, 47, 47, 25, 25, 1] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26, 58] 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, 56, 57]) total number of confs: 1418 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241833 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241833 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241833/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241833 Building REAL300025241834 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241834' /scratch/stefan/7787021/working/building/REAL300025241834 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241834 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241834/0 /scratch/stefan/7787021/working/building/REAL300025241834 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/716 `/scratch/stefan/7787021/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(C)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241834.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241834 none CCCCCC(C)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 152, 182, 38, 38, 38, 38, 35, 35, 35, 35, 33, 32, 24, 33, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 182, 182, 182, 182, 152, 152, 38, 38, 38, 35, 35, 35, 35, 35, 35, 35, 35, 35, 24, 24, 1] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26, 58] 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, 56, 57]) total number of confs: 882 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241834 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241834 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241834/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241834 Building REAL300025241835 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241835' /scratch/stefan/7787021/working/building/REAL300025241835 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241835 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241835/0 /scratch/stefan/7787021/working/building/REAL300025241835 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/717 `/scratch/stefan/7787021/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=N1) `REAL300025241835.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241835 none COC1=CN=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 199, 199, 199, 166, 162, 136, 88, 136, 71, 88, 45, 71, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 199, 166, 166, 162, 162, 136, 136, 136, 136, 88, 88, 88, 45, 45, 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: 882 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241835 none COC1=CN=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 3, 3, 3, 11, 14, 22, 22, 35, 35, 55, 55, 71, 107, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 3, 11, 11, 15, 15, 21, 22, 22, 22, 35, 35, 35, 71, 71, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 26, 30, 31] set([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: 526 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241835 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241835 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241835/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241835 Building REAL300025241836 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241836' /scratch/stefan/7787021/working/building/REAL300025241836 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241836 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241836/0 /scratch/stefan/7787021/working/building/REAL300025241836 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/718 `/scratch/stefan/7787021/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=CS1) `REAL300025241836.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241836 none CC1=C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=CS1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 153, 52, 52, 52, 52, 52, 51, 51, 51, 42, 51, 21, 41, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 153, 153, 52, 52, 52, 52, 52, 51, 51, 51, 51, 51, 51, 51, 21, 21, 1, 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]) total number of confs: 678 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241836 none CC1=C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=CS1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 12, 12, 12, 16, 16, 17, 17, 17, 17, 22, 22, 55, 94, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 3, 3, 12, 16, 16, 16, 16, 17, 17, 17, 17, 17, 17, 17, 55, 55, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 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, 44, 45]) total number of confs: 478 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241836 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241836 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241836/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241836 Building REAL300025241837 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241837' /scratch/stefan/7787021/working/building/REAL300025241837 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241837 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241837/0 /scratch/stefan/7787021/working/building/REAL300025241837 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/719 `/scratch/stefan/7787021/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)C(C)C) `REAL300025241837.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241837 none CCOC(C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)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.3', 'C.2', '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, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 176, 133, 133, 133, 130, 112, 91, 77, 91, 51, 77, 22, 50, 13, 1, 1, 1, 1, 1, 1, 1, 176, 201, 201, 176, 176, 176, 176, 176, 176, 133, 130, 130, 112, 112, 91, 91, 91, 91, 77, 77, 77, 22, 22, 1, 201, 201, 201, 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]) total number of confs: 951 number of broken/clashed sets: 111 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241837 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241837 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241837/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241837 Building REAL300025241838 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241838' /scratch/stefan/7787021/working/building/REAL300025241838 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241838 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241838/0 /scratch/stefan/7787021/working/building/REAL300025241838 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/720 `/scratch/stefan/7787021/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241838.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241838 none C#CCOCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 133, 133, 84, 84, 84, 82, 82, 60, 60, 60, 44, 60, 32, 44, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 133, 133, 133, 133, 84, 82, 82, 82, 82, 60, 60, 60, 60, 60, 60, 60, 32, 32, 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: 941 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241838 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241838 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241838/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241838 Building REAL300025241839 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241839' /scratch/stefan/7787021/working/building/REAL300025241839 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241839 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241839/0 /scratch/stefan/7787021/working/building/REAL300025241839 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/721 `/scratch/stefan/7787021/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241839.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241839 none C#CCOC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 163, 158, 126, 158, 126, 126, 93, 93, 63, 55, 63, 43, 56, 31, 43, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 158, 158, 158, 158, 126, 93, 93, 93, 93, 63, 63, 63, 63, 56, 56, 56, 31, 31, 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: 964 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241839 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241839 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241839/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241839 Building REAL300025241840 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241840' /scratch/stefan/7787021/working/building/REAL300025241840 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241840 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241840/0 /scratch/stefan/7787021/working/building/REAL300025241840 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/722 `/scratch/stefan/7787021/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[N@@H+]1CCCC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241840.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241840 none CC(C)[N@@H+]1CCCC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 188, 188, 188, 152, 152, 136, 122, 136, 99, 122, 32, 99, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 188, 152, 152, 152, 152, 136, 136, 136, 136, 122, 122, 122, 32, 32, 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: 741 number of broken/clashed sets: 117 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241840 none CC(C)[N@@H+]1CCCC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 13, 16, 16, 20, 20, 29, 29, 70, 110, 201, 201, 201, 201, 201, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 14, 14, 15, 15, 16, 16, 16, 16, 20, 20, 20, 70, 70, 201] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 39, 40, 35, 41, 36, 38, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 527 number of broken/clashed sets: 117 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241840 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241840/1 /scratch/stefan/7787021/working/building/REAL300025241840 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/723 `/scratch/stefan/7787021/working/3D/723' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[N@H+]1CCCC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241840.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241840/1/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: REAL300025241840 none CC(C)[N@H+]1CCCC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 189, 189, 189, 138, 137, 111, 104, 111, 89, 104, 35, 89, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 189, 138, 138, 137, 137, 111, 111, 111, 111, 104, 104, 104, 35, 35, 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: 752 number of broken/clashed sets: 106 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241840 none CC(C)[N@H+]1CCCC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 4, 4, 4, 12, 12, 13, 13, 17, 17, 24, 24, 62, 106, 201, 201, 201, 201, 201, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 13, 13, 13, 13, 13, 13, 17, 17, 17, 62, 62, 201] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 39, 40, 35, 41, 36, 38, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 515 number of broken/clashed sets: 106 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241840 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241840 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241840/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241840/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241840 Building REAL300025241841 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241841' /scratch/stefan/7787021/working/building/REAL300025241841 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241841 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241841/0 /scratch/stefan/7787021/working/building/REAL300025241841 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/724 `/scratch/stefan/7787021/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCOCC1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241841.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241841 none CC(CCNC(=O)CCOCC1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 31, 31, 31, 31, 31, 31, 117, 117, 126, 185, 201, 201, 18, 29, 13, 18, 8, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 117, 117, 117, 117, 185, 185, 201, 201, 201, 201, 201, 29, 29, 29, 13, 13, 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: 835 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: REAL300025241841 none CC(CCNC(=O)CCOCC1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 55, 55, 17, 55, 17, 11, 6, 1, 1, 1, 1, 86, 100, 100, 103, 103, 134, 167, 201, 201, 201, 201, 201, 86, 86, 86, 86, 86, 86, 86, 86, 55, 17, 17, 17, 17, 6, 6, 1, 1, 1, 1, 1, 100, 100, 100, 134, 134, 201] 201 rigid atoms, others: [45, 43, 41, 42, 11, 12, 13, 44, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 49, 50, 51]) total number of confs: 710 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241841 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241841 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241841/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241841 Building REAL300025241842 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241842' /scratch/stefan/7787021/working/building/REAL300025241842 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241842 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241842/0 /scratch/stefan/7787021/working/building/REAL300025241842 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/725 `/scratch/stefan/7787021/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)COC1CCOC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241842.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241842 none CC(CCNC(=O)COC1CCOC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 51, 53, 67, 78, 80, 80, 80, 147, 161, 201, 201, 201, 201, 51, 51, 28, 50, 13, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 67, 67, 78, 78, 80, 147, 147, 201, 201, 201, 201, 201, 201, 201, 51, 51, 51, 28, 28, 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: 825 number of broken/clashed sets: 142 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241842 none CC(CCNC(=O)COC1CCOC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 26, 17, 17, 8, 17, 3, 1, 1, 1, 1, 1, 1, 34, 37, 37, 39, 39, 75, 109, 201, 201, 201, 201, 201, 34, 34, 34, 34, 32, 32, 26, 26, 17, 8, 8, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 75, 75, 201] 201 rigid atoms, others: [43, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49]) total number of confs: 581 number of broken/clashed sets: 142 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241842 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241842 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241842/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241842 Building REAL300025241843 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241843' /scratch/stefan/7787021/working/building/REAL300025241843 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241843 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241843/0 /scratch/stefan/7787021/working/building/REAL300025241843 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/726 `/scratch/stefan/7787021/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)NC(N)=O) `REAL300025241843.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241843 none CC(CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 97, 93, 65, 58, 65, 46, 59, 31, 46, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 128, 97, 97, 93, 93, 65, 65, 65, 65, 59, 59, 59, 31, 31, 1, 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]) total number of confs: 901 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241843 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241843 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241843/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241843 Building REAL300025241844 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241844' /scratch/stefan/7787021/working/building/REAL300025241844 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241844 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241844/0 /scratch/stefan/7787021/working/building/REAL300025241844 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/727 `/scratch/stefan/7787021/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1(C(F)F)CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241844.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241844 none CC(CCNC(=O)C1(C(F)F)CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 5, 15, 15, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [88, 68, 88, 112, 115, 126, 126, 126, 201, 201, 201, 201, 201, 48, 68, 24, 48, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 112, 112, 115, 115, 126, 201, 201, 201, 201, 201, 68, 68, 68, 24, 24, 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: 828 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: REAL300025241844 none CC(CCNC(=O)C1(C(F)F)CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 5, 15, 15, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [17, 11, 10, 3, 3, 1, 3, 1, 1, 5, 5, 1, 1, 17, 24, 24, 32, 32, 64, 100, 201, 201, 201, 201, 201, 17, 17, 17, 17, 11, 11, 10, 10, 3, 5, 1, 1, 1, 1, 24, 24, 24, 64, 64, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 9, 10, 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]) total number of confs: 525 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241844 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241844 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241844/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241844 Building REAL300025241845 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241845' /scratch/stefan/7787021/working/building/REAL300025241845 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241845 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241845/0 /scratch/stefan/7787021/working/building/REAL300025241845 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/728 `/scratch/stefan/7787021/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCCC2(CC2)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241845.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241845 none CC(CCNC(=O)C1CCCC2(CC2)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [90, 84, 90, 91, 95, 95, 95, 95, 201, 201, 201, 201, 201, 201, 201, 63, 84, 25, 63, 13, 1, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 91, 91, 95, 95, 95, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 84, 84, 84, 25, 25, 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: 676 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: REAL300025241845 none CC(CCNC(=O)C1CCCC2(CC2)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [25, 19, 16, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 25, 28, 28, 33, 33, 67, 111, 201, 201, 201, 201, 201, 25, 25, 25, 25, 19, 19, 16, 16, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 67, 67, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 49, 50, 51, 52, 53, 54]) total number of confs: 518 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241845 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241845 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241845/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241845 Building REAL300025241846 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241846' /scratch/stefan/7787021/working/building/REAL300025241846 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241846 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241846/0 /scratch/stefan/7787021/working/building/REAL300025241846 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/729 `/scratch/stefan/7787021/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C)(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241846.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241846 none C=CCC(C)(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 93, 180, 180, 93, 93, 88, 82, 76, 76, 76, 57, 76, 28, 56, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 180, 180, 180, 180, 180, 180, 93, 88, 88, 82, 82, 76, 76, 76, 76, 76, 76, 76, 28, 28, 1] 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]) total number of confs: 900 number of broken/clashed sets: 125 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241846 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241846 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241846/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241846 Building REAL300025241847 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241847' /scratch/stefan/7787021/working/building/REAL300025241847 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241847 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241847/0 /scratch/stefan/7787021/working/building/REAL300025241847 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/730 `/scratch/stefan/7787021/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C(F)C1=CC=CC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241847.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241847 none CC(CCNC(=O)C(F)C1=CC=CC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 15, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [83, 72, 83, 99, 106, 107, 107, 107, 201, 201, 201, 201, 201, 201, 201, 53, 72, 25, 52, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 99, 99, 106, 106, 107, 201, 201, 201, 201, 201, 201, 72, 72, 72, 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: 895 number of broken/clashed sets: 79 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241847 none CC(CCNC(=O)C(F)C1=CC=CC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 15, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [17, 11, 9, 5, 5, 2, 5, 1, 2, 1, 1, 1, 1, 1, 1, 17, 21, 21, 32, 32, 67, 102, 201, 201, 201, 201, 201, 17, 17, 17, 17, 12, 12, 9, 9, 5, 2, 1, 1, 1, 1, 1, 21, 21, 21, 67, 67, 201] 201 rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47]) total number of confs: 525 number of broken/clashed sets: 79 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241847 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241847 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241847/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241847 Building REAL300025241848 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241848' /scratch/stefan/7787021/working/building/REAL300025241848 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241848 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241848/0 /scratch/stefan/7787021/working/building/REAL300025241848 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/731 `/scratch/stefan/7787021/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CC12CCC2)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241848.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241848 none CC(CCNC(=O)C1CC12CCC2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [113, 103, 113, 121, 126, 128, 128, 128, 201, 201, 201, 201, 201, 79, 103, 31, 79, 13, 1, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 121, 121, 126, 126, 128, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 103, 103, 31, 31, 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: 712 number of broken/clashed sets: 112 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241848 none CC(CCNC(=O)C1CC12CCC2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [24, 20, 18, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 24, 26, 26, 31, 31, 64, 103, 201, 201, 201, 201, 201, 24, 24, 24, 24, 20, 20, 18, 18, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 64, 64, 201] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 505 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241848 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241848 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241848/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241848 Building REAL300025241849 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241849' /scratch/stefan/7787021/working/building/REAL300025241849 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241849 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241849/0 /scratch/stefan/7787021/working/building/REAL300025241849 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/732 `/scratch/stefan/7787021/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)[C@@H]1CC(=O)NC(=O)N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241849.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241849 none CC(CCNC(=O)[C@@H]1CC(=O)NC(=O)N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 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: [77, 63, 77, 84, 100, 120, 120, 120, 201, 201, 201, 201, 201, 201, 201, 201, 43, 63, 21, 43, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 84, 84, 100, 100, 120, 201, 201, 201, 201, 63, 63, 63, 21, 21, 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: 744 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241849 none CC(CCNC(=O)[C@@H]1CC(=O)NC(=O)N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 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, 16, 14, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 26, 26, 32, 32, 63, 102, 201, 201, 201, 201, 201, 18, 18, 18, 18, 16, 16, 14, 14, 7, 1, 1, 1, 1, 26, 26, 26, 63, 63, 201] 201 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 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]) total number of confs: 496 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241849 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241849 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241849/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241849 Building REAL300025241850 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241850' /scratch/stefan/7787021/working/building/REAL300025241850 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241850 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241850/0 /scratch/stefan/7787021/working/building/REAL300025241850 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/733 `/scratch/stefan/7787021/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC(C)N1C=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241850.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241850 none CC(CCNC(=O)CC(C)N1C=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 98, 103, 107, 112, 112, 112, 112, 153, 157, 157, 201, 201, 201, 201, 84, 98, 28, 84, 13, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 107, 107, 112, 112, 112, 153, 153, 157, 157, 157, 157, 201, 201, 201, 98, 98, 98, 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: 705 number of broken/clashed sets: 115 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241850 none CC(CCNC(=O)CC(C)N1C=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [20, 18, 16, 15, 15, 7, 15, 3, 1, 3, 1, 1, 1, 1, 1, 20, 20, 20, 28, 28, 66, 105, 201, 201, 201, 201, 201, 20, 20, 20, 20, 19, 19, 16, 16, 15, 7, 7, 3, 4, 4, 4, 1, 1, 1, 20, 20, 20, 66, 66, 201] 201 rigid atoms, others: [43, 8, 44, 10, 11, 12, 13, 14, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47, 48, 49, 50]) total number of confs: 522 number of broken/clashed sets: 115 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241850 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241850 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241850/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241850 Building REAL300025241851 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241851' /scratch/stefan/7787021/working/building/REAL300025241851 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241851 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241851/0 /scratch/stefan/7787021/working/building/REAL300025241851 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/734 `/scratch/stefan/7787021/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C(C)=N1) `REAL300025241851.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241851 none CCN1C=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 132, 132, 132, 103, 98, 66, 62, 66, 49, 63, 32, 49, 13, 1, 1, 1, 1, 1, 1, 1, 150, 150, 150, 201, 201, 201, 201, 201, 150, 132, 103, 103, 98, 98, 66, 66, 66, 66, 63, 63, 63, 32, 32, 1, 150, 150, 150] 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]) total number of confs: 899 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: REAL300025241851 none CCN1C=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 11, 11, 16, 16, 17, 17, 35, 35, 47, 67, 150, 150, 150, 150, 150, 1, 1, 1, 5, 5, 5, 5, 5, 1, 4, 11, 11, 11, 11, 16, 16, 16, 16, 17, 17, 17, 47, 47, 150, 2, 2, 2] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 24, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 389 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241851 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241851 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241851/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241851 Building REAL300025241852 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241852' /scratch/stefan/7787021/working/building/REAL300025241852 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241852 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241852/0 /scratch/stefan/7787021/working/building/REAL300025241852 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/735 `/scratch/stefan/7787021/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NN1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241852.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241852 none CC1=CC=NN1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 119, 119, 119, 110, 101, 86, 70, 86, 52, 70, 29, 52, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 119, 110, 110, 101, 101, 86, 86, 86, 86, 70, 70, 70, 29, 29, 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: 920 number of broken/clashed sets: 107 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241852 none CC1=CC=NN1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 201 conformations 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, 2, 7, 7, 7, 14, 17, 24, 24, 30, 30, 40, 40, 73, 108, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 2, 2, 7, 14, 14, 17, 17, 24, 24, 24, 24, 30, 30, 30, 73, 73, 201] 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, 46, 47]) total number of confs: 569 number of broken/clashed sets: 107 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241852 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241852 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241852/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241852 Building REAL300025241853 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241853' /scratch/stefan/7787021/working/building/REAL300025241853 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241853 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241853/0 /scratch/stefan/7787021/working/building/REAL300025241853 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/736 `/scratch/stefan/7787021/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1C=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=N1) `REAL300025241853.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241853 none CCCN1C=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 144, 144, 144, 85, 85, 85, 84, 84, 56, 56, 56, 39, 56, 29, 39, 13, 1, 1, 1, 1, 1, 1, 1, 144, 144, 201, 201, 201, 201, 201, 201, 201, 144, 85, 84, 84, 84, 84, 56, 56, 56, 56, 56, 56, 56, 29, 29, 1, 144] 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]) total number of confs: 813 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: REAL300025241853 none CCCN1C=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 9, 21, 21, 31, 48, 144, 144, 144, 144, 144, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 31, 31, 144, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 2, 50, 25, 26] set([0, 1, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 308 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241853 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241853 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241853/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241853 Building REAL300025241854 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241854' /scratch/stefan/7787021/working/building/REAL300025241854 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241854 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241854/0 /scratch/stefan/7787021/working/building/REAL300025241854 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/737 `/scratch/stefan/7787021/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC(C2CC2)=NO1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241854.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241854 none CC(CCNC(=O)C1=CC(C2CC2)=NO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 25, 20, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 11, 11, 32, 34, 34, 41, 41, 86, 117, 201, 201, 201, 201, 201, 32, 32, 32, 32, 25, 25, 20, 20, 11, 11, 1, 1, 1, 1, 1, 34, 34, 34, 86, 86, 201] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 41] 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, 42, 43, 44, 45, 46, 47]) total number of confs: 585 number of broken/clashed sets: 112 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241854 none CC(CCNC(=O)C1=CC(C2CC2)=NO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [86, 81, 86, 103, 151, 160, 160, 160, 160, 160, 160, 201, 201, 160, 160, 70, 81, 28, 70, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 103, 103, 151, 151, 160, 160, 201, 201, 201, 201, 201, 81, 81, 81, 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: 863 number of broken/clashed sets: 112 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241854 none CC(CCNC(=O)C1=CC(C2CC2)=NO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [8, 5, 4, 2, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 10, 10, 12, 12, 30, 47, 160, 160, 160, 160, 160, 8, 8, 8, 8, 5, 5, 4, 4, 2, 1, 11, 11, 11, 11, 11, 10, 10, 10, 30, 30, 160] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 13, 14, 36] set([0, 1, 2, 3, 11, 12, 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, 46, 47]) total number of confs: 335 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241854 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241854 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241854/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241854 Building REAL300025241855 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241855' /scratch/stefan/7787021/working/building/REAL300025241855 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241855 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241855/0 /scratch/stefan/7787021/working/building/REAL300025241855 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/738 `/scratch/stefan/7787021/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=NO1) `REAL300025241855.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241855 none CCC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 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, 173, 173, 119, 119, 119, 117, 108, 102, 102, 102, 79, 102, 29, 79, 12, 1, 1, 1, 1, 1, 1, 1, 173, 173, 173, 201, 201, 201, 201, 201, 119, 117, 117, 108, 108, 102, 102, 102, 102, 102, 102, 102, 29, 29, 1, 173] 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]) total number of confs: 675 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241855 none CCC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 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: [5, 1, 1, 1, 1, 4, 4, 5, 7, 8, 11, 11, 11, 11, 15, 15, 41, 78, 173, 173, 173, 173, 173, 1, 1, 1, 6, 6, 6, 5, 5, 5, 7, 7, 8, 8, 11, 11, 11, 11, 11, 11, 11, 41, 41, 173, 1] 201 rigid atoms, others: [1, 2, 3, 4, 46, 23, 24, 25] set([0, 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: 402 number of broken/clashed sets: 113 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241855 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241855 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241855/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241855 Building REAL300025241856 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241856' /scratch/stefan/7787021/working/building/REAL300025241856 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241856 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241856/0 /scratch/stefan/7787021/working/building/REAL300025241856 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/739 `/scratch/stefan/7787021/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1=CSC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241856.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241856 none CC(CCNC(=O)CC1=CSC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 5, 1, 1, 14, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [88, 77, 88, 98, 111, 112, 112, 112, 201, 201, 201, 201, 201, 58, 77, 29, 58, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 98, 98, 111, 111, 112, 201, 201, 201, 201, 77, 77, 77, 29, 29, 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: 864 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: REAL300025241856 none CC(CCNC(=O)CC1=CSC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 5, 1, 1, 14, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [28, 23, 16, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 28, 32, 32, 39, 39, 71, 108, 201, 201, 201, 201, 201, 28, 28, 28, 28, 23, 23, 16, 16, 9, 3, 3, 1, 1, 32, 32, 32, 71, 71, 201] 201 rigid atoms, others: [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, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 563 number of broken/clashed sets: 124 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241856 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241856 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241856/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241856 Building REAL300025241857 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241857' /scratch/stefan/7787021/working/building/REAL300025241857 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241857 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241857/0 /scratch/stefan/7787021/working/building/REAL300025241857 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/740 `/scratch/stefan/7787021/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=COC(C2CC2)=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241857.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241857 none CC(CCNC(=O)C1=COC(C2CC2)=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 5, 5, 5, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 34, 28, 13, 13, 13, 13, 12, 12, 13, 1, 1, 1, 1, 13, 45, 47, 47, 52, 52, 95, 127, 201, 201, 201, 201, 201, 45, 45, 45, 45, 34, 34, 28, 28, 13, 13, 1, 1, 1, 1, 1, 47, 47, 47, 95, 95, 201] 201 rigid atoms, others: [37, 38, 39, 40, 41, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47]) total number of confs: 639 number of broken/clashed sets: 128 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241857 none CC(CCNC(=O)C1=COC(C2CC2)=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 5, 5, 5, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 63, 68, 95, 123, 136, 136, 136, 136, 136, 136, 136, 201, 201, 136, 58, 63, 28, 58, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 95, 95, 123, 123, 136, 136, 201, 201, 201, 201, 201, 63, 63, 63, 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: 855 number of broken/clashed sets: 128 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241857 none CC(CCNC(=O)C1=COC(C2CC2)=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 5, 5, 5, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 13, 13, 1, 8, 9, 9, 10, 10, 25, 37, 136, 136, 136, 136, 136, 8, 8, 8, 8, 6, 6, 5, 5, 2, 1, 13, 13, 13, 13, 13, 9, 9, 9, 25, 25, 136] 201 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 14] set([0, 1, 2, 3, 4, 6, 12, 13, 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, 46, 47]) total number of confs: 288 number of broken/clashed sets: 128 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241857 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241857 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241857/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241857 Building REAL300025241858 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241858' /scratch/stefan/7787021/working/building/REAL300025241858 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241858 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241858/0 /scratch/stefan/7787021/working/building/REAL300025241858 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/741 `/scratch/stefan/7787021/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=NO1) `REAL300025241858.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241858 none COCC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 12, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 98, 98, 98, 81, 81, 52, 52, 52, 41, 52, 28, 41, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 201, 201, 201, 201, 201, 98, 98, 81, 81, 81, 81, 52, 52, 52, 52, 52, 52, 52, 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: 912 number of broken/clashed sets: 101 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241858 none COCC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 12, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 2, 2, 1, 3, 3, 6, 6, 6, 6, 12, 12, 19, 34, 98, 98, 98, 98, 98, 1, 1, 12, 12, 12, 5, 5, 1, 2, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 19, 19, 98] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 25, 26] set([0, 1, 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: 241 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241858 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241858 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241858/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241858 Building REAL300025241859 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241859' /scratch/stefan/7787021/working/building/REAL300025241859 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241859 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241859/0 /scratch/stefan/7787021/working/building/REAL300025241859 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/742 `/scratch/stefan/7787021/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC(=O)N(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241859.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241859 none CC(CCNC(=O)CC(=O)N(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 68, 72, 88, 109, 120, 120, 120, 194, 201, 201, 201, 201, 60, 68, 29, 59, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 88, 88, 109, 109, 120, 194, 194, 201, 201, 201, 201, 201, 201, 68, 68, 68, 29, 29, 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: 906 number of broken/clashed sets: 132 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241859 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241859 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241859/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241859 Building REAL300025241860 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241860' /scratch/stefan/7787021/working/building/REAL300025241860 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241860 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241860/0 /scratch/stefan/7787021/working/building/REAL300025241860 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/743 `/scratch/stefan/7787021/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCN1C=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)N=N1) `REAL300025241860.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241860 none C=CCN1C=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)N=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 105, 105, 105, 105, 105, 105, 76, 76, 55, 46, 55, 35, 47, 25, 35, 12, 1, 1, 1, 1, 1, 1, 1, 105, 105, 201, 201, 201, 201, 201, 105, 105, 76, 76, 76, 76, 55, 55, 55, 55, 47, 47, 47, 25, 25, 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: 991 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241860 none C=CCN1C=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)N=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens 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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 11, 11, 20, 20, 27, 42, 105, 105, 105, 105, 105, 1, 1, 9, 9, 9, 7, 7, 1, 1, 5, 5, 5, 5, 9, 9, 9, 9, 11, 11, 11, 27, 27, 105] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 25, 26] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 273 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241860 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241860 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241860/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241860 Building REAL300025241861 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241861' /scratch/stefan/7787021/working/building/REAL300025241861 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241861 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241861/0 /scratch/stefan/7787021/working/building/REAL300025241861 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/744 `/scratch/stefan/7787021/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=NN(C)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241861.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241861 none CC(CCNC(=O)C1=NN(C)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 8, 8, 5, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [125, 109, 125, 164, 184, 201, 201, 201, 201, 201, 201, 201, 201, 63, 109, 29, 62, 13, 1, 1, 1, 1, 1, 1, 1, 125, 125, 125, 125, 164, 164, 184, 184, 201, 201, 201, 201, 201, 201, 109, 109, 109, 29, 29, 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: 841 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241861 none CC(CCNC(=O)C1=NN(C)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 8, 8, 5, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [14, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 19, 19, 32, 32, 66, 102, 201, 201, 201, 201, 201, 14, 14, 14, 14, 8, 8, 6, 6, 2, 2, 2, 2, 1, 1, 19, 19, 19, 66, 66, 201] 201 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 520 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241861 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241861 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241861/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241861 Building REAL300025241862 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241862' /scratch/stefan/7787021/working/building/REAL300025241862 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241862 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241862/0 /scratch/stefan/7787021/working/building/REAL300025241862 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/745 `/scratch/stefan/7787021/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=CN1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241862.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241862 none CC1=NC=CN1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 68, 68, 68, 68, 66, 62, 62, 62, 48, 62, 24, 47, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 169, 169, 68, 68, 68, 66, 66, 62, 62, 62, 62, 62, 62, 62, 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: 720 number of broken/clashed sets: 111 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241862 none CC1=NC=CN1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 201 conformations 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, 12, 12, 12, 14, 14, 17, 17, 17, 17, 21, 21, 54, 92, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 4, 4, 12, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 17, 54, 54, 201] 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, 46, 47]) total number of confs: 480 number of broken/clashed sets: 111 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241862 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241862/1 /scratch/stefan/7787021/working/building/REAL300025241862 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/746 `/scratch/stefan/7787021/working/3D/746' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=[NH+]C=CN1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241862.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241862/1/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: REAL300025241862 none CC1=[NH+]C=CN1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 6, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 179, 146, 146, 146, 112, 112, 86, 73, 86, 66, 73, 32, 65, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 179, 179, 146, 112, 112, 112, 112, 86, 86, 86, 86, 73, 73, 73, 32, 32, 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: 846 number of broken/clashed sets: 125 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241862 none CC1=[NH+]C=CN1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 6, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 201 conformations 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, 17, 17, 17, 28, 22, 28, 28, 31, 31, 34, 34, 88, 114, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 4, 4, 17, 28, 28, 28, 28, 28, 28, 28, 28, 31, 31, 31, 88, 88, 201] 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, 47, 48]) total number of confs: 602 number of broken/clashed sets: 125 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241862 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241862 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241862/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241862/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241862 Building REAL300025241863 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241863' /scratch/stefan/7787021/working/building/REAL300025241863 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241863 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241863/0 /scratch/stefan/7787021/working/building/REAL300025241863 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/747 `/scratch/stefan/7787021/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=N1) `REAL300025241863.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241863 none CC1=CC=C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 126, 49, 49, 49, 49, 49, 37, 36, 37, 28, 37, 22, 28, 11, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 126, 126, 49, 49, 49, 49, 49, 37, 37, 37, 37, 37, 37, 37, 22, 22, 1, 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]) total number of confs: 683 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: REAL300025241863 none CC1=CC=C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 11, 11, 11, 18, 19, 19, 19, 19, 19, 47, 47, 62, 98, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 5, 5, 11, 18, 18, 19, 19, 19, 19, 19, 19, 19, 19, 19, 62, 62, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 49, 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, 47, 48]) total number of confs: 502 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241863 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241863 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241863/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241863 Building REAL300025241864 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241864' /scratch/stefan/7787021/working/building/REAL300025241864 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241864 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241864/0 /scratch/stefan/7787021/working/building/REAL300025241864 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/748 `/scratch/stefan/7787021/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CNC(C(N)=O)=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241864.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241864 none CC(CCNC(=O)C1=CNC(C(N)=O)=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 11, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 4, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [74, 65, 74, 76, 81, 81, 81, 81, 201, 201, 201, 201, 201, 201, 201, 54, 65, 24, 54, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 76, 76, 81, 81, 81, 201, 201, 201, 201, 201, 65, 65, 65, 24, 24, 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: 483 number of broken/clashed sets: 79 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241864 none CC(CCNC(=O)C1=CNC(C(N)=O)=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 11, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 4, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 11, 10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 2, 2, 1, 14, 18, 18, 25, 25, 50, 87, 201, 201, 201, 201, 201, 14, 14, 14, 14, 12, 12, 10, 10, 5, 1, 1, 2, 2, 1, 18, 18, 18, 50, 50, 201] 201 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 14, 40, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 464 number of broken/clashed sets: 79 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241864 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241864 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241864/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241864 Building REAL300025241865 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241865' /scratch/stefan/7787021/working/building/REAL300025241865 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241865 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241865/0 /scratch/stefan/7787021/working/building/REAL300025241865 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/749 `/scratch/stefan/7787021/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241865.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241865 none CCN1C=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 138, 138, 106, 106, 106, 104, 90, 82, 75, 82, 56, 75, 22, 56, 11, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 138, 138, 138, 106, 104, 104, 90, 90, 82, 82, 82, 82, 75, 75, 75, 22, 22, 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: 851 number of broken/clashed sets: 105 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241865 none CCN1C=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 8, 11, 16, 16, 19, 19, 27, 27, 54, 81, 138, 138, 138, 138, 138, 3, 3, 3, 3, 3, 1, 1, 1, 4, 8, 8, 11, 11, 16, 16, 16, 16, 19, 19, 19, 54, 54, 138] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 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, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 397 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241865 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241865 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241865/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241865 Building REAL300025241866 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241866' /scratch/stefan/7787021/working/building/REAL300025241866 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241866 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241866/0 /scratch/stefan/7787021/working/building/REAL300025241866 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/750 `/scratch/stefan/7787021/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241866.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241866 none CC(C)N1C=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 137, 137, 137, 133, 118, 106, 101, 106, 78, 101, 28, 78, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 137, 133, 133, 118, 118, 106, 106, 106, 106, 101, 101, 101, 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: 637 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: REAL300025241866 none CC(C)N1C=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 8, 11, 17, 17, 18, 18, 27, 27, 62, 99, 201, 201, 201, 201, 201, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 8, 8, 11, 11, 17, 17, 17, 17, 18, 18, 18, 62, 62, 201] 201 rigid atoms, others: [1, 34, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 523 number of broken/clashed sets: 110 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241866 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241866 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241866/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241866 Building REAL300025241867 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241867' /scratch/stefan/7787021/working/building/REAL300025241867 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241867 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241867/0 /scratch/stefan/7787021/working/building/REAL300025241867 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/751 `/scratch/stefan/7787021/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC=NC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241867.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241867 none CCC1=NC=NC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 3, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 200, 200, 116, 200, 200, 116, 116, 116, 111, 104, 104, 104, 104, 86, 104, 30, 85, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 116, 200, 116, 111, 111, 104, 104, 104, 104, 104, 104, 104, 104, 104, 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: 742 number of broken/clashed sets: 108 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241867 none CCC1=NC=NC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 3, 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, 7, 7] 0 hydrogens 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, 8, 8, 8, 11, 13, 13, 13, 13, 13, 17, 17, 44, 85, 200, 200, 200, 200, 200, 5, 5, 5, 5, 5, 1, 1, 8, 11, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 44, 44, 200] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33] set([0, 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: 444 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241867 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241867 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241867/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241867 Building REAL300025241868 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241868' /scratch/stefan/7787021/working/building/REAL300025241868 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241868 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241868/0 /scratch/stefan/7787021/working/building/REAL300025241868 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/752 `/scratch/stefan/7787021/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1CCCOC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241868.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241868 none CC(CCNC(=O)CC1CCCOC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 59, 59, 59, 59, 178, 201, 201, 201, 201, 201, 48, 55, 26, 48, 13, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 59, 59, 59, 178, 178, 201, 201, 201, 201, 201, 201, 201, 201, 201, 55, 55, 55, 26, 26, 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: 783 number of broken/clashed sets: 107 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241868 none CC(CCNC(=O)CC1CCCOC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 17, 17, 5, 17, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 26, 26, 62, 99, 201, 201, 201, 201, 201, 21, 21, 21, 21, 21, 21, 19, 19, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 62, 62, 201] 201 rigid atoms, others: [45, 11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 44, 40, 43, 41, 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, 46, 47, 48, 49, 50, 51]) total number of confs: 489 number of broken/clashed sets: 107 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241868 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241868 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241868/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241868 Building REAL300025241869 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241869' /scratch/stefan/7787021/working/building/REAL300025241869 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241869 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241869/0 /scratch/stefan/7787021/working/building/REAL300025241869 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/753 `/scratch/stefan/7787021/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCC=CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241869.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241869 none CC(CCNC(=O)C1CCC=CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 85, 95, 110, 116, 117, 117, 117, 201, 201, 201, 201, 201, 201, 66, 85, 27, 66, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 110, 110, 116, 116, 117, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 85, 85, 85, 27, 27, 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: 707 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: REAL300025241869 none CC(CCNC(=O)C1CCC=CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 17, 14, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 22, 24, 24, 31, 31, 64, 103, 201, 201, 201, 201, 201, 22, 22, 22, 22, 17, 17, 14, 14, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 64, 64, 201] 201 rigid atoms, others: [45, 35, 36, 5, 38, 7, 8, 9, 10, 39, 12, 13, 44, 11, 40, 43, 41, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 46, 47, 48, 49, 50, 51]) total number of confs: 509 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241869 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241869 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241869/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241869 Building REAL300025241870 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241870' /scratch/stefan/7787021/working/building/REAL300025241870 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241870 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241870/0 /scratch/stefan/7787021/working/building/REAL300025241870 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/754 `/scratch/stefan/7787021/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=N1) `REAL300025241870.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241870 none CC1=NC=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 181, 159, 122, 104, 122, 66, 104, 26, 66, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 181, 181, 159, 159, 122, 122, 122, 122, 104, 104, 104, 26, 26, 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: 832 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241870 none CC1=NC=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 1, 2, 8, 10, 17, 17, 27, 27, 38, 38, 68, 103, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 2, 8, 8, 11, 11, 17, 17, 17, 17, 27, 27, 27, 68, 68, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 29, 30] set([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: 530 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241870 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241870 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241870/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241870 Building REAL300025241871 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241871' /scratch/stefan/7787021/working/building/REAL300025241871 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241871 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241871/0 /scratch/stefan/7787021/working/building/REAL300025241871 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/755 `/scratch/stefan/7787021/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCN1CCCC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241871.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241871 none CC(CCNC(=O)CCN1CCCC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 52, 65, 77, 81, 81, 81, 189, 189, 201, 201, 201, 201, 201, 45, 47, 20, 44, 13, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 65, 65, 77, 77, 81, 189, 189, 189, 189, 201, 201, 201, 201, 201, 201, 47, 47, 47, 20, 20, 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: 822 number of broken/clashed sets: 135 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241871 none CC(CCNC(=O)CCN1CCCC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 23, 15, 15, 5, 15, 5, 1, 1, 1, 1, 1, 1, 1, 38, 41, 41, 45, 45, 84, 122, 201, 201, 201, 201, 201, 38, 38, 38, 38, 31, 31, 24, 24, 15, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 41, 41, 41, 84, 84, 201] 201 rigid atoms, others: [45, 43, 8, 9, 10, 11, 12, 13, 14, 44, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48, 49, 50, 51]) total number of confs: 611 number of broken/clashed sets: 135 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241871 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241871 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241871/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241871 Building REAL300025241872 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241872' /scratch/stefan/7787021/working/building/REAL300025241872 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241872 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241872/0 /scratch/stefan/7787021/working/building/REAL300025241872 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/756 `/scratch/stefan/7787021/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241872.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241872 none CNS(=O)(=O)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 6, 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, 7] 0 hydrogens need 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, 201, 201, 118, 118, 118, 117, 107, 103, 103, 103, 92, 103, 33, 91, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 177, 177, 118, 117, 117, 107, 107, 103, 103, 103, 103, 103, 103, 103, 33, 33, 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: 833 number of broken/clashed sets: 139 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241872 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241872 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241872/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241872 Building REAL300025241873 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241873' /scratch/stefan/7787021/working/building/REAL300025241873 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241873 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241873/0 /scratch/stefan/7787021/working/building/REAL300025241873 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/757 `/scratch/stefan/7787021/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCCN1C=CC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241873.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241873 none CC(CCNC(=O)CCCN1C=CC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [47, 47, 47, 49, 49, 49, 49, 49, 146, 106, 184, 201, 201, 201, 201, 36, 47, 19, 36, 13, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 49, 49, 49, 49, 49, 146, 146, 154, 154, 173, 164, 201, 201, 201, 47, 47, 47, 19, 19, 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: 986 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: REAL300025241873 none CC(CCNC(=O)CCCN1C=CC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 23, 22, 22, 12, 22, 7, 5, 1, 1, 1, 1, 1, 1, 23, 23, 23, 24, 24, 58, 92, 201, 201, 201, 201, 201, 23, 23, 23, 23, 23, 23, 23, 23, 22, 12, 12, 7, 7, 5, 5, 1, 1, 1, 23, 23, 23, 58, 58, 201] 201 rigid atoms, others: [43, 9, 10, 11, 12, 13, 14, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47, 48, 49, 50]) total number of confs: 505 number of broken/clashed sets: 154 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241873 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241873 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241873/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241873 Building REAL300025241874 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241874' /scratch/stefan/7787021/working/building/REAL300025241874 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241874 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241874/0 /scratch/stefan/7787021/working/building/REAL300025241874 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/758 `/scratch/stefan/7787021/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1=NC=CS1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241874.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241874 none CC(CCNC(=O)CCC1=NC=CS1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 14, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [50, 50, 50, 53, 60, 60, 60, 60, 135, 143, 201, 201, 201, 201, 50, 50, 25, 49, 13, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 53, 53, 60, 60, 60, 135, 135, 143, 143, 201, 201, 50, 50, 50, 25, 25, 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: 675 number of broken/clashed sets: 151 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241874 none CC(CCNC(=O)CCC1=NC=CS1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 14, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [38, 35, 28, 22, 22, 6, 22, 3, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 74, 116, 201, 201, 201, 201, 201, 38, 38, 38, 38, 35, 35, 28, 28, 22, 6, 6, 3, 3, 1, 1, 38, 38, 38, 74, 74, 201] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 564 number of broken/clashed sets: 151 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241874 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241874 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241874/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241874 Building REAL300025241875 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241875' /scratch/stefan/7787021/working/building/REAL300025241875 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241875 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241875/0 /scratch/stefan/7787021/working/building/REAL300025241875 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/759 `/scratch/stefan/7787021/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241875.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241875 none COCCC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 103, 201, 103, 103, 83, 83, 57, 51, 57, 40, 52, 28, 40, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 83, 83, 83, 83, 57, 57, 57, 57, 52, 52, 52, 28, 28, 1] 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]) total number of confs: 911 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241875 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241875 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241875/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241875 Building REAL300025241876 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241876' /scratch/stefan/7787021/working/building/REAL300025241876 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241876 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241876/0 /scratch/stefan/7787021/working/building/REAL300025241876 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/760 `/scratch/stefan/7787021/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)C1CC1) `REAL300025241876.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241876 none CCOC(C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)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.3', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 5, 5, 5, 11, 14, 21, 21, 24, 24, 33, 33, 67, 100, 201, 201, 201, 201, 201, 1, 1, 1, 4, 4, 4, 4, 4, 4, 5, 11, 11, 14, 14, 21, 21, 21, 21, 24, 24, 24, 67, 67, 201, 1, 1, 1, 1, 1] 201 rigid atoms, others: [3, 47, 48, 49, 50, 51, 23, 24, 25] set([0, 1, 2, 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: 535 number of broken/clashed sets: 118 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241876 none CCOC(C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)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.3', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 156, 156, 156, 140, 122, 91, 80, 91, 55, 80, 25, 54, 13, 1, 1, 1, 1, 1, 1, 1, 173, 201, 201, 173, 173, 173, 173, 173, 173, 156, 140, 140, 122, 122, 91, 91, 91, 91, 80, 80, 80, 25, 25, 1, 201, 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]) total number of confs: 866 number of broken/clashed sets: 118 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241876 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241876 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241876/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241876 Building REAL300025241877 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241877' /scratch/stefan/7787021/working/building/REAL300025241877 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241877 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241877/0 /scratch/stefan/7787021/working/building/REAL300025241877 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/761 `/scratch/stefan/7787021/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCOCC(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241877.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241877 none CC(CCNC(=O)CCOCC(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 28, 28, 28, 116, 139, 145, 201, 201, 201, 22, 28, 15, 22, 11, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 116, 116, 139, 139, 201, 201, 201, 28, 28, 28, 15, 15, 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: 854 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241877 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241877 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241877/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241877 Building REAL300025241878 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241878' /scratch/stefan/7787021/working/building/REAL300025241878 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241878 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241878/0 /scratch/stefan/7787021/working/building/REAL300025241878 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/762 `/scratch/stefan/7787021/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CN1N=CN=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241878.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241878 none CC(CCNC(=O)CN1N=CN=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 5, 8, 8, 1, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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] 0 hydrogens 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, 62, 72, 72, 72, 72, 164, 201, 201, 201, 201, 54, 61, 28, 53, 12, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 62, 62, 72, 72, 72, 164, 164, 201, 61, 61, 61, 28, 28, 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: 741 number of broken/clashed sets: 141 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241878 none CC(CCNC(=O)CN1N=CN=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 5, 8, 8, 1, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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] 0 hydrogens 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, 26, 23, 23, 7, 23, 1, 1, 1, 1, 1, 1, 33, 33, 33, 34, 34, 71, 107, 201, 201, 201, 201, 201, 33, 33, 33, 33, 32, 32, 26, 26, 23, 7, 7, 1, 33, 33, 33, 71, 71, 201] 201 rigid atoms, others: [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, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 534 number of broken/clashed sets: 141 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241878 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241878 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241878/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241878 Building REAL300025241879 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241879' /scratch/stefan/7787021/working/building/REAL300025241879 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241879 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241879/0 /scratch/stefan/7787021/working/building/REAL300025241879 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/763 `/scratch/stefan/7787021/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=NC=N1) `REAL300025241879.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241879 none COC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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 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, 199, 199, 199, 166, 155, 124, 84, 124, 69, 84, 42, 69, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 199, 166, 166, 155, 155, 124, 124, 124, 124, 84, 84, 84, 42, 42, 1, 201] 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]) total number of confs: 888 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241879 none COC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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 201 conformations 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, 4, 12, 15, 23, 23, 36, 36, 57, 57, 79, 116, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 17, 17, 23, 23, 23, 23, 36, 36, 36, 79, 79, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 24, 25, 26, 27, 28, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 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: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241879 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241879 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241879/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241879 Building REAL300025241880 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241880' /scratch/stefan/7787021/working/building/REAL300025241880 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241880 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241880/0 /scratch/stefan/7787021/working/building/REAL300025241880 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/764 `/scratch/stefan/7787021/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1C[NH+]2CCC1CC2)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241880.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241880 none CC(CCNC(=O)C1C[NH+]2CCC1CC2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [125, 105, 125, 157, 160, 190, 190, 190, 190, 190, 190, 190, 190, 190, 190, 190, 91, 105, 32, 91, 13, 1, 1, 1, 1, 1, 1, 1, 125, 125, 125, 125, 157, 157, 160, 160, 190, 190, 190, 190, 190, 190, 190, 190, 190, 190, 190, 190, 190, 105, 105, 105, 32, 32, 1] 190 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: 759 number of broken/clashed sets: 118 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241880 none CC(CCNC(=O)C1C[NH+]2CCC1CC2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [20, 15, 12, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 22, 22, 31, 31, 72, 114, 190, 190, 190, 190, 190, 20, 20, 20, 20, 16, 16, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 72, 72, 190] 190 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 49, 50, 51, 52, 53, 54]) total number of confs: 516 number of broken/clashed sets: 118 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241880 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241880 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241880/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241880 Building REAL300025241881 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241881' /scratch/stefan/7787021/working/building/REAL300025241881 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241881 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241881/0 /scratch/stefan/7787021/working/building/REAL300025241881 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/765 `/scratch/stefan/7787021/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@@H](C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241881.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241881 none CCCC[C@@H](C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 60, 176, 176, 60, 60, 57, 57, 41, 41, 41, 30, 41, 21, 30, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 176, 176, 176, 60, 57, 57, 57, 57, 41, 41, 41, 41, 41, 41, 41, 21, 21, 1] 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]) total number of confs: 865 number of broken/clashed sets: 83 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241881 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241881 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241881/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241881 Building REAL300025241882 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241882' /scratch/stefan/7787021/working/building/REAL300025241882 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241882 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241882/0 /scratch/stefan/7787021/working/building/REAL300025241882 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/766 `/scratch/stefan/7787021/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=NC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1) `REAL300025241882.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241882 none CCC1=CC=NC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 103, 103, 103, 103, 103, 103, 103, 103, 98, 98, 81, 60, 81, 47, 60, 30, 47, 12, 1, 1, 1, 1, 1, 1, 1, 103, 201, 201, 201, 201, 201, 103, 103, 103, 98, 98, 98, 98, 81, 81, 81, 81, 60, 60, 60, 30, 30, 1, 103] 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, 49]) total number of confs: 1036 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241882 none CCC1=CC=NC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 6, 6, 10, 10, 14, 14, 25, 25, 36, 58, 103, 103, 103, 103, 103, 1, 3, 3, 3, 2, 2, 1, 1, 3, 6, 6, 6, 6, 10, 10, 10, 10, 14, 14, 14, 36, 36, 103, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 49, 26] set([0, 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: 277 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241882 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241882 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241882/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241882 Building REAL300025241883 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241883' /scratch/stefan/7787021/working/building/REAL300025241883 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241883 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241883/0 /scratch/stefan/7787021/working/building/REAL300025241883 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/767 `/scratch/stefan/7787021/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CC1) `REAL300025241883.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241883 none CC1=C(C)CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CC1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 70, 51, 49, 51, 39, 49, 25, 39, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 72, 71, 71, 70, 70, 51, 51, 51, 51, 49, 49, 49, 25, 25, 1, 201, 201, 201, 201] 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: 680 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: REAL300025241883 none CC1=C(C)CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CC1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 8, 8, 8, 15, 15, 17, 17, 18, 18, 40, 40, 63, 107, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 8, 15, 15, 15, 15, 17, 17, 17, 17, 18, 18, 18, 63, 63, 201, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 34, 35, 52, 53, 54, 25, 26, 51] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 533 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241883 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241883 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241883/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241883 Building REAL300025241884 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241884' /scratch/stefan/7787021/working/building/REAL300025241884 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241884 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241884/0 /scratch/stefan/7787021/working/building/REAL300025241884 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/768 `/scratch/stefan/7787021/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCCCC(C)(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241884.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241884 none CC(CCNC(=O)CCCCC(C)(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 45, 47, 47, 47, 47, 170, 162, 201, 162, 201, 201, 201, 38, 45, 26, 37, 11, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 47, 47, 47, 170, 170, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 45, 45, 45, 26, 26, 1] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26, 58] 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, 56, 57]) total number of confs: 1356 number of broken/clashed sets: 161 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241884 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241884 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241884/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241884 Building REAL300025241885 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241885' /scratch/stefan/7787021/working/building/REAL300025241885 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241885 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241885/0 /scratch/stefan/7787021/working/building/REAL300025241885 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/769 `/scratch/stefan/7787021/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(CC=C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241885.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241885 none C=CCC(CC=C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 164, 104, 38, 104, 173, 182, 38, 38, 38, 38, 38, 35, 38, 22, 35, 14, 21, 9, 1, 1, 1, 1, 1, 1, 1, 184, 184, 184, 164, 164, 104, 173, 173, 182, 182, 182, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 35, 35, 14, 14, 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: 1238 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241885 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241885 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241885/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241885 Building REAL300025241886 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241886' /scratch/stefan/7787021/working/building/REAL300025241886 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241886 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241886/0 /scratch/stefan/7787021/working/building/REAL300025241886 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/770 `/scratch/stefan/7787021/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1(C)CC=CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241886.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241886 none CC(CCNC(=O)C1(C)CC=CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 135, 154, 179, 193, 200, 200, 200, 201, 201, 201, 201, 201, 201, 80, 135, 31, 80, 13, 1, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 179, 179, 193, 193, 200, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 135, 135, 135, 31, 31, 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: 788 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: REAL300025241886 none CC(CCNC(=O)C1(C)CC=CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 10, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 16, 21, 21, 35, 35, 67, 106, 201, 201, 201, 201, 201, 16, 16, 16, 16, 12, 12, 10, 10, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 67, 67, 201] 201 rigid atoms, others: [45, 11, 5, 38, 7, 8, 9, 10, 39, 12, 13, 44, 40, 43, 41, 42] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 46, 47, 48, 49, 50, 51]) total number of confs: 515 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241886 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241886 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241886/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241886 Building REAL300025241887 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241887' /scratch/stefan/7787021/working/building/REAL300025241887 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241887 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241887/0 /scratch/stefan/7787021/working/building/REAL300025241887 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/771 `/scratch/stefan/7787021/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CS(=O)(=O)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241887.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241887 none CC(CCNC(=O)C1CS(=O)(=O)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 5, 14, 11, 11, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [88, 82, 88, 96, 101, 104, 104, 104, 201, 201, 201, 201, 201, 64, 82, 26, 64, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 96, 96, 101, 101, 104, 201, 201, 201, 201, 201, 82, 82, 82, 26, 26, 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: 682 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241887 none CC(CCNC(=O)C1CS(=O)(=O)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 5, 14, 11, 11, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [17, 14, 13, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 18, 18, 27, 27, 72, 116, 201, 201, 201, 201, 201, 17, 17, 17, 17, 14, 14, 13, 13, 8, 1, 1, 1, 1, 1, 18, 18, 18, 72, 72, 201] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44]) total number of confs: 522 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241887 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241887 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241887/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241887 Building REAL300025241888 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241888' /scratch/stefan/7787021/working/building/REAL300025241888 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241888 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241888/0 /scratch/stefan/7787021/working/building/REAL300025241888 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/772 `/scratch/stefan/7787021/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=CS1) `REAL300025241888.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241888 none CC1=C(C)C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=CS1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 87, 87, 87, 87, 82, 80, 75, 80, 56, 75, 24, 56, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 87, 87, 87, 82, 82, 80, 80, 80, 80, 75, 75, 75, 24, 24, 1, 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]) total number of confs: 493 number of broken/clashed sets: 105 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241888 none CC1=C(C)C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=CS1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations 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, 8, 8, 15, 19, 23, 23, 25, 25, 33, 33, 67, 110, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 2, 2, 2, 8, 15, 15, 19, 19, 23, 23, 23, 23, 25, 25, 25, 67, 67, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 24, 25] set([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]) total number of confs: 541 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241888 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241888 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241888/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241888 Building REAL300025241889 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241889' /scratch/stefan/7787021/working/building/REAL300025241889 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241889 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241889/0 /scratch/stefan/7787021/working/building/REAL300025241889 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/773 `/scratch/stefan/7787021/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241889.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241889 none CCC(C)(C)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 145, 201, 201, 83, 83, 83, 82, 73, 65, 64, 65, 52, 64, 26, 51, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 145, 145, 83, 82, 82, 73, 73, 65, 65, 65, 65, 64, 64, 64, 26, 26, 1] 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]) total number of confs: 876 number of broken/clashed sets: 149 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241889 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241889 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241889/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241889 Building REAL300025241890 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241890' /scratch/stefan/7787021/working/building/REAL300025241890 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241890 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241890/0 /scratch/stefan/7787021/working/building/REAL300025241890 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/774 `/scratch/stefan/7787021/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)CCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241890.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241890 none CCCC(C)CCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 129, 201, 117, 108, 32, 32, 32, 32, 26, 26, 26, 26, 26, 22, 20, 26, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 129, 129, 129, 108, 108, 32, 32, 32, 26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 20, 1] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26, 58] 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, 56, 57]) total number of confs: 1071 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241890 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241890 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241890/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241890 Building REAL300025241891 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241891' /scratch/stefan/7787021/working/building/REAL300025241891 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241891 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241891/0 /scratch/stefan/7787021/working/building/REAL300025241891 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/775 `/scratch/stefan/7787021/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CCCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241891.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241891 none CCC(C)CCCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 201, 117, 100, 107, 39, 39, 39, 39, 32, 32, 32, 32, 32, 25, 25, 32, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 117, 117, 117, 117, 117, 117, 107, 107, 39, 39, 39, 32, 32, 32, 32, 32, 32, 32, 32, 32, 25, 25, 1] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26, 58] 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, 56, 57]) total number of confs: 1177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241891 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241891 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241891/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241891 Building REAL300025241892 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241892' /scratch/stefan/7787021/working/building/REAL300025241892 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241892 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241892/0 /scratch/stefan/7787021/working/building/REAL300025241892 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/776 `/scratch/stefan/7787021/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241892.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241892 none CC(C)C(C)(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 112, 201, 201, 112, 112, 112, 106, 87, 73, 87, 54, 73, 26, 53, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 112, 112, 112, 106, 106, 87, 87, 87, 87, 73, 73, 73, 26, 26, 1] 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]) total number of confs: 974 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241892 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241892 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241892/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241892 Building REAL300025241893 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241893' /scratch/stefan/7787021/working/building/REAL300025241893 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241893 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241893/0 /scratch/stefan/7787021/working/building/REAL300025241893 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/777 `/scratch/stefan/7787021/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(Cl)C(C)(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241893.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241893 none C=C(Cl)C(C)(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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: [1, 1, 16, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 201, 100, 187, 187, 100, 100, 99, 89, 78, 67, 78, 50, 67, 24, 49, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 187, 187, 187, 187, 187, 187, 100, 99, 99, 89, 89, 78, 78, 78, 78, 67, 67, 67, 24, 24, 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: 962 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241893 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241893 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241893/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241893 Building REAL300025241894 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241894' /scratch/stefan/7787021/working/building/REAL300025241894 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241894 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241894/0 /scratch/stefan/7787021/working/building/REAL300025241894 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/778 `/scratch/stefan/7787021/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1N=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241894.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241894 none CC(C)N1N=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 162, 162, 162, 159, 144, 138, 133, 138, 99, 133, 32, 99, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 159, 159, 144, 144, 138, 138, 138, 138, 133, 133, 133, 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: 675 number of broken/clashed sets: 99 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241894 none CC(C)N1N=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 10, 13, 17, 17, 18, 18, 23, 23, 46, 81, 201, 201, 201, 201, 201, 4, 4, 4, 4, 4, 4, 4, 1, 1, 4, 10, 10, 13, 13, 17, 17, 17, 17, 18, 18, 18, 46, 46, 201] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35] 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 447 number of broken/clashed sets: 99 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241894 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241894 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241894/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241894 Building REAL300025241895 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241895' /scratch/stefan/7787021/working/building/REAL300025241895 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241895 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241895/0 /scratch/stefan/7787021/working/building/REAL300025241895 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/779 `/scratch/stefan/7787021/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(C)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241895.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241895 none C=CC(C)(C)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 201, 201, 108, 108, 108, 103, 93, 71, 64, 71, 52, 64, 29, 51, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 168, 168, 108, 103, 103, 93, 93, 71, 71, 71, 71, 64, 64, 64, 29, 29, 1] 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]) total number of confs: 973 number of broken/clashed sets: 145 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241895 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241895 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241895/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241895 Building REAL300025241896 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241896' /scratch/stefan/7787021/working/building/REAL300025241896 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241896 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241896/0 /scratch/stefan/7787021/working/building/REAL300025241896 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/780 `/scratch/stefan/7787021/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=CC(C)=N1) `REAL300025241896.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241896 none CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=CC(C)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 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] 0 hydrogens need 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, 128, 128, 128, 128, 123, 109, 91, 109, 68, 91, 29, 67, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 128, 201, 201, 201, 201, 128, 128, 128, 123, 123, 109, 109, 109, 109, 91, 91, 91, 29, 29, 1, 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]) total number of confs: 868 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: REAL300025241896 none CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=CC(C)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 9, 10, 18, 18, 22, 22, 28, 28, 59, 99, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 1, 3, 9, 9, 12, 12, 18, 18, 18, 18, 22, 22, 22, 59, 59, 201, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 46, 23, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 514 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241896 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241896 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241896/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241896 Building REAL300025241897 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241897' /scratch/stefan/7787021/working/building/REAL300025241897 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241897 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241897/0 /scratch/stefan/7787021/working/building/REAL300025241897 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/781 `/scratch/stefan/7787021/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CN1N=CC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241897.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241897 none CC(CCNC(=O)CN1N=CC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [70, 70, 70, 87, 102, 103, 103, 103, 201, 201, 201, 201, 201, 51, 70, 30, 51, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 87, 87, 102, 102, 103, 201, 201, 201, 201, 70, 70, 70, 30, 30, 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: 895 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: REAL300025241897 none CC(CCNC(=O)CN1N=CC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [24, 19, 15, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 24, 27, 27, 29, 29, 65, 103, 201, 201, 201, 201, 201, 24, 24, 24, 24, 19, 19, 15, 15, 9, 3, 3, 1, 1, 27, 27, 27, 65, 65, 201] 201 rigid atoms, others: [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, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 540 number of broken/clashed sets: 141 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241897 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241897 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241897/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241897 Building REAL300025241898 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241898' /scratch/stefan/7787021/working/building/REAL300025241898 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241898 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241898/0 /scratch/stefan/7787021/working/building/REAL300025241898 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/782 `/scratch/stefan/7787021/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)S1) `REAL300025241898.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241898 none CC1=CC(C)=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)S1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 121, 121, 121, 120, 108, 88, 76, 88, 54, 76, 25, 53, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 121, 120, 120, 108, 108, 88, 88, 88, 88, 76, 76, 76, 25, 25, 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: 655 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241898 none CC1=CC(C)=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)S1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 9, 12, 19, 19, 24, 24, 33, 33, 69, 104, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 2, 2, 2, 5, 9, 9, 12, 12, 19, 19, 19, 19, 24, 24, 24, 69, 69, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 29] set([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, 45, 46, 47]) total number of confs: 552 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241898 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241898 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241898/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241898 Building REAL300025241899 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241899' /scratch/stefan/7787021/working/building/REAL300025241899 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241899 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241899/0 /scratch/stefan/7787021/working/building/REAL300025241899 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/783 `/scratch/stefan/7787021/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1=CNN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241899.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241899 none CC(CCNC(=O)CCC1=CNN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 90, 92, 96, 101, 102, 102, 102, 197, 201, 201, 201, 201, 201, 75, 90, 28, 75, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 96, 96, 101, 101, 102, 197, 197, 201, 201, 201, 201, 201, 90, 90, 90, 28, 28, 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: 821 number of broken/clashed sets: 98 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241899 none CC(CCNC(=O)CCC1=CNN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 30, 27, 17, 17, 5, 17, 2, 1, 1, 1, 1, 1, 1, 32, 32, 32, 34, 34, 66, 107, 201, 201, 201, 201, 201, 32, 32, 32, 32, 31, 31, 28, 28, 17, 5, 5, 2, 2, 1, 1, 1, 32, 32, 32, 66, 66, 201] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46, 47]) total number of confs: 537 number of broken/clashed sets: 143 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241899 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241899 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241899/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241899 Building REAL300025241900 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241900' /scratch/stefan/7787021/working/building/REAL300025241900 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241900 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241900/0 /scratch/stefan/7787021/working/building/REAL300025241900 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/784 `/scratch/stefan/7787021/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CNC=N1)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241900.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241900 none CC(CC1=CNC=N1)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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, 7, 7, 4, 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, 7, 7, 7, 7] 0 hydrogens 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, 89, 167, 189, 201, 201, 201, 201, 89, 89, 82, 82, 55, 55, 55, 42, 55, 30, 42, 13, 1, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 189, 189, 201, 201, 201, 89, 82, 82, 82, 82, 55, 55, 55, 55, 55, 55, 55, 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: 906 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: REAL300025241900 none CC(CC1=CNC=N1)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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, 7, 7, 4, 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, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 8, 17, 17, 17, 18, 18, 22, 22, 22, 22, 48, 48, 65, 103, 201, 201, 201, 201, 201, 8, 8, 8, 8, 5, 5, 1, 1, 1, 17, 18, 18, 18, 18, 22, 22, 22, 22, 22, 22, 22, 65, 65, 201] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 35] 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, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 508 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241900 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241900/1 /scratch/stefan/7787021/working/building/REAL300025241900 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/785 `/scratch/stefan/7787021/working/3D/785' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CN=CN1)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241900.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241900/1/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: REAL300025241900 none CC(CC1=CN=CN1)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7] 0 hydrogens 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, 103, 199, 201, 201, 201, 201, 201, 103, 103, 79, 78, 57, 47, 57, 34, 47, 25, 34, 13, 1, 1, 1, 1, 1, 1, 1, 199, 199, 199, 199, 201, 201, 201, 201, 201, 103, 79, 79, 78, 78, 57, 57, 57, 57, 47, 47, 47, 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: 893 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: REAL300025241900 none CC(CC1=CN=CN1)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 22, 24, 35, 35, 39, 39, 64, 64, 82, 111, 201, 201, 201, 201, 201, 5, 5, 5, 5, 3, 3, 1, 1, 1, 10, 22, 22, 24, 24, 35, 35, 35, 35, 39, 39, 39, 82, 82, 201] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 35] 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, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 582 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241900 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241900 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241900/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241900/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241900 Building REAL300025241901 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241901' /scratch/stefan/7787021/working/building/REAL300025241901 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241901 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241901/0 /scratch/stefan/7787021/working/building/REAL300025241901 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/786 `/scratch/stefan/7787021/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)[C@@H]1C[C@H]1C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241901.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241901 none CC(CCNC(=O)[C@@H]1C[C@H]1C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [34, 33, 30, 24, 24, 5, 24, 5, 5, 5, 1, 5, 1, 1, 1, 34, 36, 36, 37, 37, 76, 110, 201, 201, 201, 201, 201, 34, 34, 34, 34, 33, 33, 30, 30, 24, 5, 5, 1, 1, 1, 1, 1, 36, 36, 36, 76, 76, 201] 201 rigid atoms, others: [38, 39, 40, 41, 10, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 531 number of broken/clashed sets: 153 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241901 none CC(CCNC(=O)[C@@H]1C[C@H]1C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [68, 67, 68, 81, 89, 90, 90, 90, 200, 200, 200, 200, 200, 201, 201, 67, 67, 31, 67, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 81, 81, 89, 89, 90, 200, 200, 201, 201, 201, 201, 201, 67, 67, 67, 31, 31, 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: 686 number of broken/clashed sets: 153 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241901 none CC(CCNC(=O)[C@@H]1C[C@H]1C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [17, 16, 14, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 5, 5, 17, 19, 19, 20, 20, 44, 67, 200, 200, 200, 200, 200, 17, 17, 17, 17, 16, 16, 14, 14, 10, 1, 1, 5, 5, 5, 5, 5, 19, 19, 19, 44, 44, 200] 201 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 418 number of broken/clashed sets: 153 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241901 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241901 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241901/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241901 Building REAL300025241902 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241902' /scratch/stefan/7787021/working/building/REAL300025241902 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241902 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241902/0 /scratch/stefan/7787021/working/building/REAL300025241902 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/787 `/scratch/stefan/7787021/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)[C@@H]1C[C@H]1C1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241902.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241902 none CC(CCNC(=O)[C@@H]1C[C@H]1C1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [25, 20, 17, 13, 13, 2, 13, 2, 2, 2, 1, 2, 1, 1, 1, 1, 25, 25, 25, 27, 27, 61, 99, 201, 201, 201, 201, 201, 25, 25, 25, 25, 21, 21, 17, 17, 13, 2, 2, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 61, 61, 201] 201 rigid atoms, others: [45, 39, 40, 41, 10, 43, 12, 13, 14, 15, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 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]) total number of confs: 500 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241902 none CC(CCNC(=O)[C@@H]1C[C@H]1C1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [73, 70, 73, 82, 88, 89, 89, 89, 201, 201, 201, 201, 201, 201, 201, 201, 63, 70, 31, 63, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73, 82, 82, 88, 88, 89, 201, 201, 201, 201, 201, 201, 201, 201, 201, 70, 70, 70, 31, 31, 1] 201 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: 691 number of broken/clashed sets: 124 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241902 none CC(CCNC(=O)[C@@H]1C[C@H]1C1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [23, 18, 15, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 23, 23, 23, 25, 25, 57, 96, 201, 201, 201, 201, 201, 23, 23, 23, 23, 19, 19, 15, 15, 11, 1, 1, 2, 2, 2, 2, 2, 2, 2, 23, 23, 23, 57, 57, 201] 201 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 5] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 494 number of broken/clashed sets: 124 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241902 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241902 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241902/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241902 Building REAL300025241903 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241903' /scratch/stefan/7787021/working/building/REAL300025241903 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241903 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241903/0 /scratch/stefan/7787021/working/building/REAL300025241903 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/788 `/scratch/stefan/7787021/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)[C@@H]1OCC[C@@H]1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241903.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241903 none C=C(C)[C@@H]1OCC[C@@H]1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', '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, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 201, 201, 201, 201, 163, 149, 114, 103, 114, 64, 103, 30, 64, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 163, 163, 149, 149, 114, 114, 114, 114, 103, 103, 103, 30, 30, 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: 810 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: REAL300025241903 none C=C(C)[C@@H]1OCC[C@@H]1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', '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, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 10, 12, 18, 18, 26, 26, 42, 42, 71, 111, 201, 201, 201, 201, 201, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 10, 10, 12, 12, 18, 18, 18, 18, 26, 26, 26, 71, 71, 201] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35, 36, 37] set([0, 2, 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: 513 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241903 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241903 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241903/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241903 Building REAL300025241904 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241904' /scratch/stefan/7787021/working/building/REAL300025241904 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241904 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241904/0 /scratch/stefan/7787021/working/building/REAL300025241904 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/789 `/scratch/stefan/7787021/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C(C)C1=CC=NN1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241904.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241904 none CC(CCNC(=O)C(C)C1=CC=NN1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 8, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [78, 77, 78, 83, 90, 91, 91, 91, 195, 195, 201, 201, 201, 201, 201, 64, 77, 25, 64, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 83, 83, 90, 90, 91, 195, 195, 195, 195, 201, 201, 201, 201, 201, 77, 77, 77, 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: 813 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: REAL300025241904 none CC(CCNC(=O)C(C)C1=CC=NN1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 8, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [22, 19, 18, 14, 14, 5, 14, 1, 5, 1, 1, 1, 1, 1, 1, 22, 22, 22, 27, 27, 66, 99, 201, 201, 201, 201, 201, 22, 22, 22, 22, 20, 20, 18, 18, 14, 5, 5, 5, 5, 1, 1, 2, 2, 2, 22, 22, 22, 66, 66, 201] 201 rigid atoms, others: [7, 40, 9, 10, 11, 12, 13, 14, 41] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 516 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241904 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241904 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241904/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241904 Building REAL300025241905 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241905' /scratch/stefan/7787021/working/building/REAL300025241905 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241905 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241905/0 /scratch/stefan/7787021/working/building/REAL300025241905 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/790 `/scratch/stefan/7787021/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CN2CCCC2=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241905.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241905 none CC(CCNC(=O)C1=CN2CCCC2=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [115, 103, 115, 158, 174, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 60, 103, 25, 60, 13, 1, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 158, 158, 174, 174, 201, 201, 201, 201, 201, 201, 201, 201, 103, 103, 103, 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: 843 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: REAL300025241905 none CC(CCNC(=O)C1=CN2CCCC2=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [13, 8, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 21, 21, 36, 36, 70, 108, 201, 201, 201, 201, 201, 13, 13, 13, 13, 9, 9, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 70, 70, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 36, 38, 42, 39, 37] set([0, 1, 2, 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]) total number of confs: 520 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241905 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241905 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241905/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241905 Building REAL300025241906 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241906' /scratch/stefan/7787021/working/building/REAL300025241906 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241906 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241906/0 /scratch/stefan/7787021/working/building/REAL300025241906 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/791 `/scratch/stefan/7787021/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)[C@@H]1CC[N@H+](C)[C@@H]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241906.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241906 none CC(CCNC(=O)[C@@H]1CC[N@H+](C)[C@@H]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 9, 6, 5, 5, 7, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [149, 143, 149, 180, 180, 200, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 201, 113, 143, 34, 113, 13, 1, 1, 1, 1, 1, 1, 1, 149, 149, 149, 149, 180, 180, 180, 180, 200, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 143, 143, 143, 34, 34, 1] 201 rigid atoms, others: [53, 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]) total number of confs: 731 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: REAL300025241906 none CC(CCNC(=O)[C@@H]1CC[N@H+](C)[C@@H]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 9, 6, 5, 5, 7, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 11, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 21, 21, 27, 27, 64, 113, 201, 201, 201, 201, 201, 17, 17, 17, 17, 14, 14, 11, 11, 4, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 21, 21, 21, 64, 64, 201] 201 rigid atoms, others: [11, 5, 38, 7, 8, 9, 10, 39, 12, 13, 14, 15, 16, 40, 41] set([0, 1, 2, 3, 4, 6, 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, 51, 52, 53]) total number of confs: 533 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241906 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241906/1 /scratch/stefan/7787021/working/building/REAL300025241906 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/792 `/scratch/stefan/7787021/working/3D/792' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)[C@@H]1CC[N@@H+](C)[C@@H]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241906.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241906/1/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: REAL300025241906 none CC(CCNC(=O)[C@@H]1CC[N@@H+](C)[C@@H]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 9, 6, 5, 5, 7, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [28, 27, 28, 29, 29, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 27, 27, 14, 27, 8, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 29, 29, 29, 29, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 27, 27, 27, 14, 14, 1] 32 rigid atoms, others: [53, 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]) total number of confs: 106 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: REAL300025241906 none CC(CCNC(=O)[C@@H]1CC[N@@H+](C)[C@@H]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 9, 6, 5, 5, 7, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 11, 11, 13, 13, 19, 24, 32, 32, 32, 32, 32, 10, 10, 10, 10, 9, 9, 7, 7, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 11, 11, 11, 19, 19, 32] 32 rigid atoms, others: [11, 5, 38, 7, 8, 9, 10, 39, 12, 13, 14, 15, 16, 40, 41] set([0, 1, 2, 3, 4, 6, 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, 51, 52, 53]) total number of confs: 119 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241906 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241906 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241906/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241906/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241906 Building REAL300025241907 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241907' /scratch/stefan/7787021/working/building/REAL300025241907 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241907 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241907/0 /scratch/stefan/7787021/working/building/REAL300025241907 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/793 `/scratch/stefan/7787021/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)[C@@H]1C[C@H]1CC(C)(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241907.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241907 none CC(CCNC(=O)[C@@H]1C[C@H]1CC(C)(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 69, 75, 84, 90, 90, 90, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201, 61, 69, 29, 61, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 84, 84, 90, 90, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 69, 69, 69, 29, 29, 1] 201 rigid atoms, others: [56, 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, 54, 55]) total number of confs: 657 number of broken/clashed sets: 142 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241907 none CC(CCNC(=O)[C@@H]1C[C@H]1CC(C)(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 16, 14, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 20, 20, 20, 21, 21, 49, 80, 201, 201, 201, 201, 201, 20, 20, 20, 20, 17, 17, 14, 14, 11, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 49, 49, 201] 201 rigid atoms, others: [11, 5, 38, 7, 8, 9, 10, 39, 12] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 466 number of broken/clashed sets: 142 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241907 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241907 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241907/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241907 Building REAL300025241908 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241908' /scratch/stefan/7787021/working/building/REAL300025241908 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241908 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241908/0 /scratch/stefan/7787021/working/building/REAL300025241908 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/794 `/scratch/stefan/7787021/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CC[N@@H+]1C) `REAL300025241908.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241908 none CC[C@@H]1[C@@H](C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 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 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 25, 25, 25, 23, 25, 21, 23, 17, 21, 11, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 25, 25, 25, 25, 25, 25, 25, 25, 23, 23, 23, 17, 17, 1, 31, 31, 31, 31, 31, 31, 31] 31 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, 54, 55, 56]) total number of confs: 103 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241908 none CC[C@@H]1[C@@H](C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 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 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 6, 8, 8, 8, 8, 10, 10, 15, 19, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 15, 15, 31, 1, 1, 1, 1, 2, 2, 2] 31 rigid atoms, others: [1, 2, 3, 4, 5, 6, 50, 51, 52, 53, 25, 26, 27, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 54, 55, 56]) total number of confs: 111 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241908 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241908/1 /scratch/stefan/7787021/working/building/REAL300025241908 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/795 `/scratch/stefan/7787021/working/3D/795' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CC[N@H+]1C) `REAL300025241908.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241908/1/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: REAL300025241908 none CC[C@@H]1[C@@H](C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 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 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 87, 74, 87, 74, 74, 70, 70, 58, 56, 58, 51, 56, 32, 51, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 74, 70, 70, 70, 70, 58, 58, 58, 58, 56, 56, 56, 32, 32, 1, 87, 87, 87, 87, 87, 87, 87] 87 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, 54, 55, 56]) total number of confs: 342 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: REAL300025241908 none CC[C@@H]1[C@@H](C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 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 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 7, 9, 9, 10, 10, 10, 10, 30, 43, 87, 87, 87, 87, 87, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 4, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 30, 30, 87, 1, 1, 1, 1, 2, 2, 2] 87 rigid atoms, others: [1, 2, 3, 4, 5, 6, 50, 51, 52, 53, 25, 26, 27, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 54, 55, 56]) total number of confs: 234 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241908 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241908 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241908/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241908/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241908 Building REAL300025241909 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241909' /scratch/stefan/7787021/working/building/REAL300025241909 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241909 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241909/0 /scratch/stefan/7787021/working/building/REAL300025241909 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/796 `/scratch/stefan/7787021/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)[C@@H]1C[C@@H]2C=C[C@H]1CC2)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241909.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241909 none CC(CCNC(=O)[C@@H]1C[C@@H]2C=C[C@H]1CC2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 5, 7, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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: [114, 100, 114, 131, 135, 136, 136, 136, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 73, 100, 29, 73, 13, 1, 1, 1, 1, 1, 1, 1, 114, 114, 114, 114, 131, 131, 135, 135, 136, 201, 201, 201, 201, 201, 201, 201, 201, 100, 100, 100, 29, 29, 1] 201 rigid atoms, others: [52, 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]) total number of confs: 754 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241909 none CC(CCNC(=O)[C@@H]1C[C@@H]2C=C[C@H]1CC2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 5, 7, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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: [22, 17, 16, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 27, 27, 33, 33, 68, 109, 201, 201, 201, 201, 201, 22, 22, 22, 22, 18, 18, 16, 16, 9, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 68, 68, 201] 201 rigid atoms, others: [45, 11, 17, 5, 7, 8, 9, 10, 39, 12, 13, 14, 15, 16, 40, 44, 46, 43, 41, 42] set([0, 1, 2, 3, 4, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 48, 49, 50, 51, 52]) total number of confs: 515 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241909 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241909 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241909/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241909 Building REAL300025241910 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241910' /scratch/stefan/7787021/working/building/REAL300025241910 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241910 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241910/0 /scratch/stefan/7787021/working/building/REAL300025241910 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/797 `/scratch/stefan/7787021/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=CC(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=N1) `REAL300025241910.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241910 none CCN1C=CC(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 115, 115, 115, 115, 115, 63, 63, 63, 62, 62, 46, 45, 46, 34, 46, 24, 34, 12, 1, 1, 1, 1, 1, 1, 1, 115, 201, 201, 201, 201, 201, 115, 115, 115, 115, 63, 62, 62, 62, 62, 46, 46, 46, 46, 46, 46, 46, 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: 990 number of broken/clashed sets: 83 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241910 none CCN1C=CC(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 7, 7, 7, 9, 9, 11, 11, 11, 11, 25, 25, 33, 50, 115, 115, 115, 115, 115, 1, 5, 5, 5, 5, 5, 1, 1, 5, 5, 7, 9, 9, 9, 9, 11, 11, 11, 11, 11, 11, 11, 33, 33, 115] 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, 49, 50]) total number of confs: 287 number of broken/clashed sets: 83 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241910 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241910 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241910/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241910 Building REAL300025241911 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241911' /scratch/stefan/7787021/working/building/REAL300025241911 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241911 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241911/0 /scratch/stefan/7787021/working/building/REAL300025241911 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/798 `/scratch/stefan/7787021/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1C(C)OC(C)C1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241911.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241911 none CC(CCNC(=O)C1C(C)OC(C)C1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 127, 146, 175, 190, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 127, 30, 79, 13, 1, 1, 1, 1, 1, 1, 1, 146, 146, 146, 146, 175, 175, 190, 190, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 127, 127, 127, 30, 30, 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: 783 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241911 none CC(CCNC(=O)C1C(C)OC(C)C1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 14, 21, 21, 38, 38, 63, 102, 201, 201, 201, 201, 201, 14, 14, 14, 14, 9, 9, 8, 8, 2, 1, 1, 2, 2, 2, 1, 2, 2, 2, 1, 2, 2, 2, 21, 21, 21, 63, 63, 201] 201 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 45, 41, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 511 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241911 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241911 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241911/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241911 Building REAL300025241912 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241912' /scratch/stefan/7787021/working/building/REAL300025241912 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241912 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241912/0 /scratch/stefan/7787021/working/building/REAL300025241912 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/799 `/scratch/stefan/7787021/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(CC)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241912.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241912 none CCC(C)(CC)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 200, 191, 200, 200, 200, 191, 191, 179, 168, 137, 118, 137, 79, 118, 30, 78, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 200, 200, 200, 201, 201, 201, 201, 201, 191, 179, 179, 168, 168, 137, 137, 137, 137, 118, 118, 118, 30, 30, 1] 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]) total number of confs: 826 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241912 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241912 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241912/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241912 Building REAL300025241913 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241913' /scratch/stefan/7787021/working/building/REAL300025241913 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241913 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241913/0 /scratch/stefan/7787021/working/building/REAL300025241913 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/800 `/scratch/stefan/7787021/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1CCC(C)O1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241913.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241913 none CC(CCNC(=O)CCC1CCC(C)O1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 65, 83, 99, 110, 113, 113, 113, 201, 201, 201, 201, 201, 201, 201, 51, 65, 27, 50, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 99, 99, 110, 110, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 65, 65, 65, 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: 857 number of broken/clashed sets: 133 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241913 none CC(CCNC(=O)CCC1CCC(C)O1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 10, 10, 4, 10, 3, 1, 1, 1, 1, 1, 1, 1, 22, 26, 26, 33, 33, 67, 105, 201, 201, 201, 201, 201, 22, 22, 22, 22, 19, 19, 15, 15, 10, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 26, 26, 26, 67, 67, 201] 201 rigid atoms, others: [45, 43, 8, 9, 10, 11, 12, 13, 14, 44, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 554 number of broken/clashed sets: 133 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241913 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241913 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241913/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241913 Building REAL300025241914 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241914' /scratch/stefan/7787021/working/building/REAL300025241914 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241914 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241914/0 /scratch/stefan/7787021/working/building/REAL300025241914 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/801 `/scratch/stefan/7787021/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C12CCC(CC1)CC2)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241914.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241914 none CC(CCNC(=O)C12CCC(CC1)CC2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [128, 100, 128, 167, 188, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 69, 100, 30, 68, 13, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 128, 167, 167, 188, 188, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 100, 100, 100, 30, 30, 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: 865 number of broken/clashed sets: 115 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241914 none CC(CCNC(=O)C12CCC(CC1)CC2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [13, 8, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 18, 18, 25, 25, 61, 101, 201, 201, 201, 201, 201, 13, 13, 13, 13, 10, 10, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 61, 61, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 49, 50, 51, 52, 53, 54]) total number of confs: 509 number of broken/clashed sets: 115 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241914 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241914 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241914/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241914 Building REAL300025241915 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241915' /scratch/stefan/7787021/working/building/REAL300025241915 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241915 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241915/0 /scratch/stefan/7787021/working/building/REAL300025241915 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/802 `/scratch/stefan/7787021/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(C)(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241915.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241915 none CCCCCC(C)(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 186, 110, 186, 186, 110, 110, 88, 88, 58, 54, 58, 40, 55, 30, 40, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 192, 192, 192, 192, 186, 186, 186, 186, 186, 186, 110, 88, 88, 88, 88, 58, 58, 58, 58, 55, 55, 55, 30, 30, 1] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26, 58] 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, 56, 57]) total number of confs: 983 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241915 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241915 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241915/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241915 Building REAL300025241916 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241916' /scratch/stefan/7787021/working/building/REAL300025241916 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241916 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241916/0 /scratch/stefan/7787021/working/building/REAL300025241916 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/803 `/scratch/stefan/7787021/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(CC)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241916.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241916 none CCCCCC(CC)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 151, 87, 151, 151, 87, 87, 80, 80, 52, 47, 52, 37, 48, 26, 37, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 151, 151, 151, 151, 151, 151, 87, 80, 80, 80, 80, 52, 52, 52, 52, 48, 48, 48, 26, 26, 1] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26, 58] 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, 56, 57]) total number of confs: 999 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241916 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241916 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241916/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241916 Building REAL300025241917 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241917' /scratch/stefan/7787021/working/building/REAL300025241917 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241917 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241917/0 /scratch/stefan/7787021/working/building/REAL300025241917 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/804 `/scratch/stefan/7787021/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CCC(C)(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CC1) `REAL300025241917.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241917 none CC1=CCC(C)(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CC1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 196, 196, 125, 124, 104, 66, 104, 54, 67, 35, 54, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 196, 125, 125, 124, 124, 104, 104, 104, 104, 67, 67, 67, 35, 35, 1, 201, 201, 201, 201] 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: 814 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: REAL300025241917 none CC1=CCC(C)(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CC1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 11, 12, 18, 18, 31, 31, 47, 47, 67, 105, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 11, 11, 12, 12, 18, 18, 18, 18, 31, 31, 31, 67, 67, 201, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 51, 52, 53, 54, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 517 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241917 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241917 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241917/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241917 Building REAL300025241918 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241918' /scratch/stefan/7787021/working/building/REAL300025241918 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241918 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241918/0 /scratch/stefan/7787021/working/building/REAL300025241918 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/805 `/scratch/stefan/7787021/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C(C)(C)CC(C)(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241918.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241918 none CC(CCNC(=O)C(C)(C)CC(C)(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 90, 113, 132, 156, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 56, 90, 26, 55, 13, 1, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 132, 132, 156, 156, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 90, 90, 26, 26, 1] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26, 58] 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, 56, 57]) total number of confs: 819 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241918 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241918 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241918/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241918 Building REAL300025241919 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241919' /scratch/stefan/7787021/working/building/REAL300025241919 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241919 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241919/0 /scratch/stefan/7787021/working/building/REAL300025241919 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/806 `/scratch/stefan/7787021/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CCCCC1) `REAL300025241919.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241919 none CCC1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CCCCC1 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.3', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 109, 109, 109, 98, 93, 82, 71, 82, 51, 71, 24, 50, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 109, 98, 98, 93, 93, 82, 82, 82, 82, 71, 71, 71, 24, 24, 1, 201, 201, 201, 201, 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: 785 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: REAL300025241919 none CCC1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CCCCC1 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.3', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 11, 11, 17, 17, 23, 23, 32, 32, 59, 98, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 3, 11, 11, 13, 13, 17, 17, 17, 17, 23, 23, 23, 59, 59, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 54, 55, 56, 47, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 499 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241919 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241919 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241919/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241919 Building REAL300025241920 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241920' /scratch/stefan/7787021/working/building/REAL300025241920 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241920 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241920/0 /scratch/stefan/7787021/working/building/REAL300025241920 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/807 `/scratch/stefan/7787021/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C(C)=N1) `REAL300025241920.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241920 none CC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C(C)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 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, 201, 201, 201, 115, 115, 115, 114, 111, 88, 64, 88, 54, 65, 35, 54, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 115, 114, 114, 111, 111, 88, 88, 88, 88, 65, 65, 65, 35, 35, 1, 201, 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]) total number of confs: 637 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: REAL300025241920 none CC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C(C)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 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: [1, 1, 1, 1, 1, 1, 9, 9, 9, 18, 18, 21, 21, 23, 23, 52, 52, 75, 111, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 9, 18, 18, 18, 18, 21, 21, 21, 21, 23, 23, 23, 75, 75, 201, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 555 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241920 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241920 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241920/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241920 Building REAL300025241921 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241921' /scratch/stefan/7787021/working/building/REAL300025241921 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241921 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241921/0 /scratch/stefan/7787021/working/building/REAL300025241921 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/808 `/scratch/stefan/7787021/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1N=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241921.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241921 none CCCN1N=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 163, 163, 163, 163, 163, 90, 90, 90, 89, 87, 60, 56, 60, 39, 56, 30, 39, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 163, 163, 90, 89, 89, 87, 87, 60, 60, 60, 60, 56, 56, 56, 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: 741 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241921 none CCCN1N=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 4, 4, 4, 10, 10, 13, 13, 13, 13, 25, 25, 35, 55, 163, 163, 163, 163, 163, 4, 4, 4, 4, 4, 4, 4, 1, 1, 4, 10, 10, 10, 10, 13, 13, 13, 13, 13, 13, 13, 35, 35, 163] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 34, 35] 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 349 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241921 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241921 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241921/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241921 Building REAL300025241922 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241922' /scratch/stefan/7787021/working/building/REAL300025241922 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241922 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241922/0 /scratch/stefan/7787021/working/building/REAL300025241922 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/809 `/scratch/stefan/7787021/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1C=CC=CC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241922.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241922 none CC(CCNC(=O)C1C=CC=CC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [119, 99, 119, 138, 144, 156, 156, 156, 201, 201, 201, 201, 201, 201, 65, 99, 29, 64, 13, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 138, 138, 144, 144, 156, 201, 201, 201, 201, 201, 201, 201, 99, 99, 99, 29, 29, 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: 787 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: REAL300025241922 none CC(CCNC(=O)C1C=CC=CC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [20, 14, 12, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 20, 27, 27, 36, 36, 65, 104, 201, 201, 201, 201, 201, 20, 20, 20, 20, 16, 16, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 65, 65, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47]) total number of confs: 520 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241922 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241922 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241922/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241922 Building REAL300025241923 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241923' /scratch/stefan/7787021/working/building/REAL300025241923 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241923 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241923/0 /scratch/stefan/7787021/working/building/REAL300025241923 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/810 `/scratch/stefan/7787021/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241923.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241923 none C=C(C)CCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 84, 84, 84, 84, 79, 61, 60, 61, 59, 60, 28, 58, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 84, 84, 84, 79, 79, 61, 61, 61, 61, 60, 60, 60, 28, 28, 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: 863 number of broken/clashed sets: 168 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241923 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241923 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241923/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241923 Building REAL300025241924 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241924' /scratch/stefan/7787021/working/building/REAL300025241924 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241924 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241924/0 /scratch/stefan/7787021/working/building/REAL300025241924 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/811 `/scratch/stefan/7787021/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1=CC=NC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241924.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241924 none CC(CCNC(=O)CCC1=CC=NC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 60, 74, 94, 94, 94, 180, 187, 201, 201, 201, 201, 201, 47, 51, 27, 47, 13, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 60, 60, 74, 74, 94, 180, 180, 187, 187, 201, 201, 201, 51, 51, 51, 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: 833 number of broken/clashed sets: 141 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241924 none CC(CCNC(=O)CCC1=CC=NC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 27, 21, 21, 9, 21, 6, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 34, 34, 77, 115, 201, 201, 201, 201, 201, 32, 32, 32, 32, 29, 29, 27, 27, 21, 9, 9, 6, 6, 1, 1, 1, 32, 32, 32, 77, 77, 201] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48]) total number of confs: 570 number of broken/clashed sets: 141 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241924 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241924 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241924/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241924 Building REAL300025241925 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241925' /scratch/stefan/7787021/working/building/REAL300025241925 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241925 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241925/0 /scratch/stefan/7787021/working/building/REAL300025241925 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/812 `/scratch/stefan/7787021/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1=NN(C)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241925.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241925 none CC(CCNC(=O)CCC1=NN(C)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 8, 5, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [93, 75, 93, 113, 126, 128, 128, 128, 183, 191, 201, 201, 201, 201, 201, 57, 75, 29, 56, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 113, 113, 126, 126, 128, 183, 183, 191, 191, 201, 201, 201, 201, 201, 75, 75, 75, 29, 29, 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: 913 number of broken/clashed sets: 142 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241925 none CC(CCNC(=O)CCC1=NN(C)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 8, 5, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 20, 19, 16, 16, 8, 16, 5, 1, 1, 1, 1, 1, 1, 1, 23, 26, 26, 31, 31, 68, 105, 201, 201, 201, 201, 201, 23, 23, 23, 23, 20, 20, 19, 19, 16, 8, 8, 5, 5, 2, 2, 2, 1, 1, 26, 26, 26, 68, 68, 201] 201 rigid atoms, others: [43, 8, 9, 10, 11, 12, 13, 14, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50]) total number of confs: 556 number of broken/clashed sets: 142 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241925 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241925 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241925/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241925 Building REAL300025241926 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241926' /scratch/stefan/7787021/working/building/REAL300025241926 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241926 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241926/0 /scratch/stefan/7787021/working/building/REAL300025241926 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/813 `/scratch/stefan/7787021/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1=CC=NN1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241926.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241926 none CC(CCNC(=O)CCC1=CC=NN1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 8, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [63, 63, 63, 63, 66, 66, 66, 66, 176, 176, 201, 201, 201, 201, 201, 53, 63, 22, 53, 12, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 63, 66, 66, 66, 176, 176, 176, 176, 201, 201, 201, 201, 201, 63, 63, 63, 22, 22, 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: 733 number of broken/clashed sets: 115 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241926 none CC(CCNC(=O)CCC1=CC=NN1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 8, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 21, 19, 19, 3, 19, 3, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 29, 29, 71, 120, 201, 201, 201, 201, 201, 23, 23, 23, 23, 23, 23, 21, 21, 19, 3, 3, 3, 3, 1, 1, 2, 2, 2, 23, 23, 23, 71, 71, 201] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 523 number of broken/clashed sets: 115 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241926 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241926 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241926/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241926 Building REAL300025241927 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241927' /scratch/stefan/7787021/working/building/REAL300025241927 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241927 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241927/0 /scratch/stefan/7787021/working/building/REAL300025241927 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/814 `/scratch/stefan/7787021/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC2=C(C=CO2)N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241927.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241927 none CC(CCNC(=O)C1=CC2=C(C=CO2)N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 6, 7, 7, 7, 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: [124, 108, 124, 158, 178, 193, 193, 193, 201, 201, 201, 201, 201, 201, 201, 75, 108, 27, 74, 13, 1, 1, 1, 1, 1, 1, 1, 124, 124, 124, 124, 158, 158, 178, 178, 193, 201, 201, 201, 201, 108, 108, 108, 27, 27, 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: 789 number of broken/clashed sets: 89 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241927 none CC(CCNC(=O)C1=CC2=C(C=CO2)N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 6, 7, 7, 7, 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: [15, 11, 10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 23, 23, 31, 31, 61, 103, 201, 201, 201, 201, 201, 15, 15, 15, 15, 11, 11, 10, 10, 5, 1, 1, 1, 1, 23, 23, 23, 61, 61, 201] 201 rigid atoms, others: [36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 39, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45]) total number of confs: 482 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241927 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241927 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241927/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241927 Building REAL300025241928 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241928' /scratch/stefan/7787021/working/building/REAL300025241928 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241928 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241928/0 /scratch/stefan/7787021/working/building/REAL300025241928 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/815 `/scratch/stefan/7787021/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=NS1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241928.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241928 none CC(CCNC(=O)C1=CC=NS1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 1, 1, 1, 8, 14, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 89, 103, 124, 147, 159, 159, 159, 201, 201, 201, 201, 66, 89, 30, 66, 13, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 124, 124, 147, 147, 159, 201, 201, 89, 89, 89, 30, 30, 1] 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]) total number of confs: 739 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241928 none CC(CCNC(=O)C1=CC=NS1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 1, 1, 1, 8, 14, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 13, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 19, 23, 23, 32, 32, 58, 96, 201, 201, 201, 201, 201, 19, 19, 19, 19, 14, 14, 11, 11, 5, 1, 1, 23, 23, 23, 58, 58, 201] 201 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 486 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241928 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241928 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241928/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241928 Building REAL300025241929 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241929' /scratch/stefan/7787021/working/building/REAL300025241929 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241929 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241929/0 /scratch/stefan/7787021/working/building/REAL300025241929 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/816 `/scratch/stefan/7787021/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C(CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)OCC) `REAL300025241929.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241929 none C=C(C)C(CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)OCC 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 144, 144, 144, 102, 100, 85, 63, 85, 48, 64, 32, 48, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 144, 102, 102, 100, 100, 85, 85, 85, 85, 64, 64, 64, 32, 32, 1, 201, 201, 201, 201, 201] 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, 54]) total number of confs: 851 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241929 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241929 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241929/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241929 Building REAL300025241930 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241930' /scratch/stefan/7787021/working/building/REAL300025241930 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241930 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241930/0 /scratch/stefan/7787021/working/building/REAL300025241930 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/817 `/scratch/stefan/7787021/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CCC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)O1) `REAL300025241930.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241930 none CCC1CCC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 164, 164, 164, 132, 132, 105, 78, 105, 61, 79, 40, 61, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 164, 132, 132, 132, 132, 105, 105, 105, 105, 79, 79, 79, 40, 40, 1] 201 rigid atoms, others: [51, 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, 50]) total number of confs: 861 number of broken/clashed sets: 83 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241930 none CCC1CCC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 12, 12, 16, 16, 22, 22, 38, 38, 57, 93, 201, 201, 201, 201, 201, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 16, 16, 16, 16, 22, 22, 22, 57, 57, 201] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 34, 35, 25, 36, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 484 number of broken/clashed sets: 83 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241930 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241930 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241930/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241930 Building REAL300025241931 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241931' /scratch/stefan/7787021/working/building/REAL300025241931 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241931 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241931/0 /scratch/stefan/7787021/working/building/REAL300025241931 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/818 `/scratch/stefan/7787021/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CC1) `REAL300025241931.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241931 none COCCC1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 198, 98, 98, 98, 72, 72, 46, 46, 46, 35, 46, 22, 35, 13, 1, 1, 1, 1, 1, 1, 1, 198, 198, 201, 201, 201, 201, 201, 201, 201, 98, 72, 72, 72, 72, 46, 46, 46, 46, 46, 46, 46, 22, 22, 1, 198, 198, 198, 198] 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: 739 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: REAL300025241931 none COCCC1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 5, 1, 1, 1, 5, 5, 5, 8, 8, 13, 13, 13, 13, 31, 31, 50, 86, 198, 198, 198, 198, 198, 1, 1, 10, 10, 10, 7, 7, 5, 5, 5, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 50, 50, 198, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 48, 49, 50, 51, 24, 25] set([0, 1, 2, 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: 501 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241931 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241931 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241931/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241931 Building REAL300025241932 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241932' /scratch/stefan/7787021/working/building/REAL300025241932 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241932 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241932/0 /scratch/stefan/7787021/working/building/REAL300025241932 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/819 `/scratch/stefan/7787021/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CC1) `REAL300025241932.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241932 none CC(C)CC1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 108, 108, 108, 93, 87, 75, 63, 75, 44, 63, 23, 44, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 108, 93, 93, 87, 87, 75, 75, 75, 75, 63, 63, 63, 23, 23, 1, 201, 201, 201, 201] 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: 776 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: REAL300025241932 none CC(C)CC1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 20, 20, 26, 26, 33, 33, 64, 103, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 14, 14, 16, 16, 20, 20, 20, 20, 26, 26, 26, 64, 64, 201, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 50, 51, 52, 53, 24, 25] set([0, 1, 2, 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, 48, 49]) total number of confs: 516 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241932 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241932 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241932/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241932 Building REAL300025241933 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241933' /scratch/stefan/7787021/working/building/REAL300025241933 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241933 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241933/0 /scratch/stefan/7787021/working/building/REAL300025241933 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/820 `/scratch/stefan/7787021/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=NN1C) `REAL300025241933.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241933 none CC1=C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=NN1C 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 58, 58, 58, 58, 57, 43, 42, 43, 30, 43, 23, 30, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 142, 142, 58, 58, 58, 57, 57, 43, 43, 43, 43, 43, 43, 43, 23, 23, 1, 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]) total number of confs: 730 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241933 none CC1=C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=NN1C 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 19, 19, 19, 23, 25, 25, 25, 25, 25, 58, 58, 67, 100, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 6, 6, 19, 23, 23, 25, 25, 25, 25, 25, 25, 25, 25, 25, 67, 67, 201, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 47, 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, 48, 49, 50]) total number of confs: 497 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241933 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241933 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241933/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241933 Building REAL300025241934 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241934' /scratch/stefan/7787021/working/building/REAL300025241934 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241934 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241934/0 /scratch/stefan/7787021/working/building/REAL300025241934 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/821 `/scratch/stefan/7787021/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=C(C2CC2)C=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241934.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241934 none CC(CCNC(=O)C1=C(C2CC2)C=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 23, 15, 15, 6, 15, 6, 1, 1, 1, 1, 6, 6, 6, 31, 32, 32, 34, 34, 67, 103, 201, 201, 201, 201, 201, 31, 31, 31, 31, 25, 25, 23, 23, 15, 1, 1, 1, 1, 1, 6, 6, 6, 32, 32, 32, 67, 67, 201] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 40] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 512 number of broken/clashed sets: 131 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241934 none CC(CCNC(=O)C1=C(C2CC2)C=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 62, 65, 80, 97, 101, 101, 101, 169, 169, 201, 201, 169, 169, 169, 53, 62, 24, 53, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 80, 80, 97, 97, 101, 201, 201, 201, 201, 201, 169, 169, 169, 62, 62, 62, 24, 24, 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: 641 number of broken/clashed sets: 131 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241934 none CC(CCNC(=O)C1=C(C2CC2)C=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 15, 9, 9, 1, 9, 1, 1, 1, 6, 6, 1, 1, 1, 21, 22, 22, 24, 24, 51, 80, 169, 169, 169, 169, 169, 21, 21, 21, 21, 16, 16, 15, 15, 9, 6, 6, 6, 6, 6, 1, 1, 1, 22, 22, 22, 51, 51, 169] 201 rigid atoms, others: [5, 7, 8, 9, 42, 43, 12, 13, 14, 41] set([0, 1, 2, 3, 4, 6, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48, 49]) total number of confs: 421 number of broken/clashed sets: 131 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241934 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241934 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241934/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241934 Building REAL300025241935 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241935' /scratch/stefan/7787021/working/building/REAL300025241935 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241935 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241935/0 /scratch/stefan/7787021/working/building/REAL300025241935 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/822 `/scratch/stefan/7787021/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)C(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241935.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241935 none COCC(C)C(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 162, 162, 114, 162, 114, 114, 88, 88, 60, 54, 60, 44, 55, 27, 44, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 162, 162, 162, 162, 162, 162, 162, 162, 114, 88, 88, 88, 88, 60, 60, 60, 60, 55, 55, 55, 27, 27, 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: 953 number of broken/clashed sets: 97 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241935 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241935 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241935/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241935 Building REAL300025241936 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241936' /scratch/stefan/7787021/working/building/REAL300025241936 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241936 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241936/0 /scratch/stefan/7787021/working/building/REAL300025241936 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/823 `/scratch/stefan/7787021/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC(F)F)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241936.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241936 none CCC(CC(F)F)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 185, 69, 185, 200, 201, 201, 69, 69, 68, 65, 64, 58, 64, 38, 58, 20, 37, 12, 1, 1, 1, 1, 1, 1, 1, 192, 192, 192, 192, 192, 185, 200, 200, 201, 69, 68, 68, 65, 65, 64, 64, 64, 64, 58, 58, 58, 20, 20, 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: 1064 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241936 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241936 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241936/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241936 Building REAL300025241937 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241937' /scratch/stefan/7787021/working/building/REAL300025241937 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241937 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241937/0 /scratch/stefan/7787021/working/building/REAL300025241937 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/824 `/scratch/stefan/7787021/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C(C)(C)CC(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241937.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241937 none CC(CCNC(=O)C(C)(C)CC(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 15, 15, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [71, 68, 71, 79, 87, 99, 99, 99, 191, 191, 191, 201, 201, 201, 55, 68, 25, 54, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 79, 79, 87, 87, 99, 191, 191, 191, 191, 191, 191, 201, 201, 201, 68, 68, 68, 25, 25, 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: 911 number of broken/clashed sets: 98 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241937 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241937 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241937/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241937 Building REAL300025241938 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241938' /scratch/stefan/7787021/working/building/REAL300025241938 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241938 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241938/0 /scratch/stefan/7787021/working/building/REAL300025241938 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/825 `/scratch/stefan/7787021/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1CCC(=O)NC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241938.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241938 none CC(CCNC(=O)CC1CCC(=O)NC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 56, 56, 56, 56, 176, 201, 201, 201, 201, 201, 201, 45, 52, 22, 44, 13, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 56, 56, 56, 176, 176, 201, 201, 201, 201, 201, 201, 201, 201, 52, 52, 52, 22, 22, 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: 761 number of broken/clashed sets: 116 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241938 none CC(CCNC(=O)CC1CCC(=O)NC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 19, 19, 5, 19, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 28, 28, 66, 103, 201, 201, 201, 201, 201, 23, 23, 23, 23, 23, 23, 22, 22, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 66, 66, 201] 201 rigid atoms, others: [45, 11, 38, 7, 8, 9, 10, 39, 12, 13, 14, 44, 40, 43, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 46, 47, 48, 49, 50, 51]) total number of confs: 500 number of broken/clashed sets: 116 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241938 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241938 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241938/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241938 Building REAL300025241939 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241939' /scratch/stefan/7787021/working/building/REAL300025241939 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241939 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241939/0 /scratch/stefan/7787021/working/building/REAL300025241939 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/826 `/scratch/stefan/7787021/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1CC2CCC1O2)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241939.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241939 none CC(CCNC(=O)CC1CC2CCC1O2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 66, 66, 66, 66, 186, 201, 201, 201, 201, 201, 201, 52, 62, 26, 52, 12, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 62, 62, 66, 66, 66, 186, 186, 201, 201, 201, 201, 201, 201, 201, 201, 201, 62, 62, 62, 26, 26, 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: 770 number of broken/clashed sets: 118 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241939 none CC(CCNC(=O)CC1CC2CCC1O2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 19, 19, 5, 19, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 29, 29, 67, 106, 201, 201, 201, 201, 201, 25, 25, 25, 25, 25, 25, 21, 21, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 67, 67, 201] 201 rigid atoms, others: [45, 11, 38, 7, 8, 9, 10, 39, 12, 13, 14, 44, 40, 46, 43, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 518 number of broken/clashed sets: 118 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241939 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241939 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241939/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241939 Building REAL300025241940 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241940' /scratch/stefan/7787021/working/building/REAL300025241940 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241940 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241940/0 /scratch/stefan/7787021/working/building/REAL300025241940 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/827 `/scratch/stefan/7787021/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=NC(C)=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241940.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241940 none CCN1N=NC(C)=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 115, 115, 115, 115, 115, 115, 60, 60, 60, 57, 50, 47, 47, 47, 35, 47, 18, 34, 11, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 115, 115, 115, 60, 57, 57, 50, 50, 47, 47, 47, 47, 47, 47, 47, 18, 18, 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: 839 number of broken/clashed sets: 115 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241940 none CCN1N=NC(C)=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 9, 11, 15, 15, 15, 15, 19, 19, 35, 55, 115, 115, 115, 115, 115, 5, 5, 5, 5, 5, 2, 2, 2, 5, 9, 9, 11, 11, 15, 15, 15, 15, 15, 15, 15, 35, 35, 115] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 313 number of broken/clashed sets: 115 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241940 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241940 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241940/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241940 Building REAL300025241941 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241941' /scratch/stefan/7787021/working/building/REAL300025241941 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241941 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241941/0 /scratch/stefan/7787021/working/building/REAL300025241941 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/828 `/scratch/stefan/7787021/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NOC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241941.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241941 none CC(C)C1=NOC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 153, 153, 153, 152, 143, 134, 118, 134, 83, 118, 32, 83, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 153, 152, 152, 143, 143, 134, 134, 134, 134, 118, 118, 118, 32, 32, 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: 675 number of broken/clashed sets: 97 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241941 none CC(C)C1=NOC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 1, 6, 6, 7, 13, 14, 19, 19, 23, 23, 29, 29, 53, 91, 201, 201, 201, 201, 201, 2, 2, 2, 1, 2, 2, 2, 1, 7, 13, 13, 15, 15, 19, 19, 19, 19, 23, 23, 23, 53, 53, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 486 number of broken/clashed sets: 97 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241941 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241941 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241941/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241941 Building REAL300025241942 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241942' /scratch/stefan/7787021/working/building/REAL300025241942 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241942 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241942/0 /scratch/stefan/7787021/working/building/REAL300025241942 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/829 `/scratch/stefan/7787021/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1CCNC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241942.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241942 none CC(CCNC(=O)CC1CCNC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 74, 75, 93, 119, 126, 126, 126, 197, 201, 201, 201, 201, 201, 62, 74, 28, 62, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 93, 93, 119, 119, 126, 197, 197, 201, 201, 201, 201, 201, 201, 74, 74, 74, 28, 28, 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: 862 number of broken/clashed sets: 118 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241942 none CC(CCNC(=O)CC1CCNC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 14, 14, 5, 14, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 35, 35, 72, 110, 201, 201, 201, 201, 201, 29, 29, 29, 29, 24, 24, 22, 22, 14, 5, 5, 1, 1, 1, 1, 1, 1, 29, 29, 29, 72, 72, 201] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 40, 41, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 556 number of broken/clashed sets: 118 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241942 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241942 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241942/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241942 Building REAL300025241943 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241943' /scratch/stefan/7787021/working/building/REAL300025241943 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241943 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241943/0 /scratch/stefan/7787021/working/building/REAL300025241943 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/830 `/scratch/stefan/7787021/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)[C@]12C[C@H]1COC2)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241943.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241943 none CC(CCNC(=O)[C@]12C[C@H]1COC2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 12, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 65, 74, 81, 94, 96, 96, 96, 201, 201, 201, 201, 201, 201, 49, 65, 23, 49, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 81, 81, 94, 94, 96, 201, 201, 201, 201, 201, 201, 65, 65, 65, 23, 23, 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: 553 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: REAL300025241943 none CC(CCNC(=O)[C@]12C[C@H]1COC2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 12, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 10, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 16, 20, 20, 29, 29, 58, 101, 201, 201, 201, 201, 201, 16, 16, 16, 16, 11, 11, 9, 9, 4, 1, 1, 1, 1, 1, 1, 20, 20, 20, 58, 58, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46]) total number of confs: 493 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241943 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241943 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241943/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241943 Building REAL300025241944 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241944' /scratch/stefan/7787021/working/building/REAL300025241944 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL300025241944 as failed and skipping /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `/scratch/stefan/7787021/failed' `/scratch/stefan/7787021/working/building/REAL300025241944' -> `/scratch/stefan/7787021/failed/REAL300025241944' Building REAL300025241945 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241945' /scratch/stefan/7787021/working/building/REAL300025241945 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241945 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241945/0 /scratch/stefan/7787021/working/building/REAL300025241945 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/831 `/scratch/stefan/7787021/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241945.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241945 none CC1=C(F)C=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 119, 119, 119, 117, 111, 103, 93, 103, 69, 93, 25, 69, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 119, 117, 117, 111, 111, 103, 103, 103, 103, 93, 93, 93, 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: 570 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241945 none CC1=C(F)C=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 1, 1, 8, 8, 8, 14, 15, 20, 20, 25, 25, 31, 31, 72, 115, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 8, 14, 14, 16, 16, 20, 20, 20, 20, 25, 25, 25, 72, 72, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 30, 31] set([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: 541 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241945 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241945 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241945/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241945 Building REAL300025241946 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241946' /scratch/stefan/7787021/working/building/REAL300025241946 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241946 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241946/0 /scratch/stefan/7787021/working/building/REAL300025241946 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/832 `/scratch/stefan/7787021/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1(C)CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241946.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241946 none CC(CCNC(=O)C1(C)CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 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, 7, 7] 0 hydrogens 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, 62, 81, 104, 112, 112, 112, 112, 201, 201, 201, 42, 62, 24, 41, 12, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 104, 104, 112, 112, 112, 201, 201, 201, 201, 201, 201, 201, 62, 62, 62, 24, 24, 1] 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]) total number of confs: 829 number of broken/clashed sets: 117 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241946 none CC(CCNC(=O)C1(C)CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 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, 7, 7] 0 hydrogens 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, 12, 12, 7, 7, 1, 7, 1, 1, 1, 1, 20, 27, 27, 33, 33, 68, 105, 201, 201, 201, 201, 201, 20, 20, 20, 20, 14, 14, 12, 12, 7, 2, 2, 2, 1, 1, 1, 1, 27, 27, 27, 68, 68, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 37] set([0, 1, 2, 3, 4, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 544 number of broken/clashed sets: 117 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241946 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241946 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241946/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241946 Building REAL300025241947 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241947' /scratch/stefan/7787021/working/building/REAL300025241947 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241947 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241947/0 /scratch/stefan/7787021/working/building/REAL300025241947 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/833 `/scratch/stefan/7787021/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1F) `REAL300025241947.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241947 none CC1=CC=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1F 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 201, 201, 190, 190, 190, 169, 154, 127, 105, 127, 71, 105, 27, 71, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 190, 169, 169, 154, 154, 127, 127, 127, 127, 105, 105, 105, 27, 27, 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: 831 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: REAL300025241947 none CC1=CC=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1F 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 4, 14, 15, 22, 22, 32, 32, 40, 40, 75, 109, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 4, 14, 14, 16, 16, 22, 22, 22, 22, 32, 32, 32, 75, 75, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 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: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241947 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241947 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241947/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241947 Building REAL300025241948 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241948' /scratch/stefan/7787021/working/building/REAL300025241948 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241948 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241948/0 /scratch/stefan/7787021/working/building/REAL300025241948 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/834 `/scratch/stefan/7787021/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1CCCC1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241948.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241948 none CC(CCNC(=O)CC1CCCC1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 103, 109, 115, 120, 121, 121, 121, 201, 201, 201, 201, 201, 201, 82, 103, 29, 82, 13, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 109, 115, 115, 120, 120, 121, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 103, 103, 29, 29, 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: 877 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: REAL300025241948 none CC(CCNC(=O)CC1CCCC1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 16, 15, 8, 8, 2, 8, 1, 1, 1, 1, 1, 1, 1, 20, 24, 24, 29, 29, 62, 103, 201, 201, 201, 201, 201, 20, 20, 20, 20, 17, 17, 15, 15, 8, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 24, 24, 24, 62, 62, 201] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 44, 40, 43, 41, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 514 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241948 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241948 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241948/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241948 Building REAL300025241949 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241949' /scratch/stefan/7787021/working/building/REAL300025241949 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241949 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241949/0 /scratch/stefan/7787021/working/building/REAL300025241949 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/835 `/scratch/stefan/7787021/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241949.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241949 none CCC(=O)NC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 6] dock color type numbers: [7, 7, 7, 6, 4, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 148, 148, 148, 148, 112, 148, 112, 112, 94, 94, 64, 63, 64, 48, 64, 31, 48, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 148, 148, 148, 148, 148, 112, 94, 94, 94, 94, 64, 64, 64, 64, 64, 64, 64, 31, 31, 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: 998 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241949 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241949 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241949/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241949 Building REAL300025241950 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241950' /scratch/stefan/7787021/working/building/REAL300025241950 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241950 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241950/0 /scratch/stefan/7787021/working/building/REAL300025241950 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/836 `/scratch/stefan/7787021/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CN(C)C(=O)C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241950.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241950 none CC(CCNC(=O)CN(C)C(=O)C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 31, 31, 31, 102, 149, 149, 164, 164, 201, 201, 16, 22, 11, 16, 8, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 23, 23, 31, 102, 102, 149, 149, 149, 201, 201, 201, 201, 201, 22, 22, 22, 11, 11, 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: 753 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: REAL300025241950 none CC(CCNC(=O)CN(C)C(=O)C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 35, 35, 16, 35, 7, 5, 7, 1, 5, 1, 1, 1, 42, 42, 42, 59, 59, 102, 136, 201, 201, 201, 201, 201, 42, 42, 42, 42, 42, 42, 42, 42, 35, 16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 42, 42, 42, 102, 102, 201] 201 rigid atoms, others: [45, 41, 10, 43, 12, 13, 14, 44, 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, 39, 40, 46, 47, 48, 49, 50, 51]) total number of confs: 615 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241950 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241950 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241950/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241950 Building REAL300025241951 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241951' /scratch/stefan/7787021/working/building/REAL300025241951 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241951 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241951/0 /scratch/stefan/7787021/working/building/REAL300025241951 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/837 `/scratch/stefan/7787021/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CC(=O)N(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241951.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241951 none CC(CCNC(=O)C1CC(=O)N(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 90, 105, 126, 142, 155, 155, 155, 201, 201, 201, 201, 201, 201, 57, 90, 30, 57, 13, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 126, 126, 142, 142, 155, 201, 201, 201, 201, 201, 201, 201, 201, 90, 90, 90, 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: 808 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241951 none CC(CCNC(=O)C1CC(=O)N(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 24, 24, 29, 29, 60, 102, 201, 201, 201, 201, 201, 17, 17, 17, 17, 16, 16, 15, 15, 8, 1, 1, 1, 2, 2, 2, 1, 1, 24, 24, 24, 60, 60, 201] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 41, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 43, 44, 45, 46, 47, 48]) total number of confs: 503 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241951 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241951 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241951/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241951 Building REAL300025241952 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241952' /scratch/stefan/7787021/working/building/REAL300025241952 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241952 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241952/0 /scratch/stefan/7787021/working/building/REAL300025241952 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/838 `/scratch/stefan/7787021/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CC1=O) `REAL300025241952.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241952 none CCN1CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 116, 116, 116, 86, 86, 86, 85, 85, 78, 63, 78, 48, 64, 34, 48, 12, 1, 1, 1, 1, 1, 1, 1, 116, 116, 116, 201, 201, 201, 201, 201, 116, 116, 116, 86, 85, 85, 85, 85, 78, 78, 78, 78, 64, 64, 64, 34, 34, 1, 116, 116] 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]) total number of confs: 966 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241952 none CCN1CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 8, 8, 14, 14, 15, 15, 17, 17, 32, 32, 41, 61, 116, 116, 116, 116, 116, 1, 1, 1, 3, 3, 3, 2, 2, 1, 1, 1, 8, 14, 14, 14, 14, 15, 15, 15, 15, 17, 17, 17, 41, 41, 116, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 34, 50, 51, 24, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 300 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241952 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241952 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241952/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241952 Building REAL300025241953 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241953' /scratch/stefan/7787021/working/building/REAL300025241953 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241953 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241953/0 /scratch/stefan/7787021/working/building/REAL300025241953 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/839 `/scratch/stefan/7787021/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241953.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241953 none CNC(=O)NCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 4, 7, 6, 4, 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, 7, 7] 0 hydrogens need 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, 77, 77, 77, 71, 71, 50, 46, 50, 36, 47, 28, 36, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 198, 198, 77, 71, 71, 71, 71, 50, 50, 50, 50, 47, 47, 47, 28, 28, 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: 855 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241953 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241953 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241953/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241953 Building REAL300025241954 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241954' /scratch/stefan/7787021/working/building/REAL300025241954 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241954 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241954/0 /scratch/stefan/7787021/working/building/REAL300025241954 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/840 `/scratch/stefan/7787021/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)SC=C1) `REAL300025241954.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241954 none CCC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)SC=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 100, 100, 100, 99, 83, 72, 65, 72, 49, 65, 20, 49, 10, 1, 1, 1, 1, 1, 1, 1, 151, 151, 151, 201, 201, 201, 201, 201, 100, 99, 99, 83, 83, 72, 72, 72, 72, 65, 65, 65, 20, 20, 1, 151, 151] 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]) total number of confs: 806 number of broken/clashed sets: 106 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241954 none CCC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)SC=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 7, 10, 16, 16, 19, 19, 27, 27, 55, 83, 151, 151, 151, 151, 151, 1, 1, 1, 3, 3, 3, 3, 3, 3, 7, 7, 10, 10, 16, 16, 16, 16, 19, 19, 19, 55, 55, 151, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 46, 47, 23, 24, 25] set([0, 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: 430 number of broken/clashed sets: 106 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241954 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241954 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241954/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241954 Building REAL300025241955 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241955' /scratch/stefan/7787021/working/building/REAL300025241955 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241955 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241955/0 /scratch/stefan/7787021/working/building/REAL300025241955 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/841 `/scratch/stefan/7787021/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C[NH+]1C(C)CCC1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241955.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241955 none CC(CCNC(=O)C[NH+]1C(C)CCC1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 115, 130, 151, 151, 194, 194, 194, 201, 201, 201, 201, 201, 201, 201, 201, 96, 115, 34, 96, 13, 1, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 151, 151, 151, 151, 194, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 115, 115, 115, 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: 777 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: REAL300025241955 none CC(CCNC(=O)C[NH+]1C(C)CCC1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 13, 14, 6, 6, 3, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 21, 21, 30, 30, 71, 120, 201, 201, 201, 201, 201, 16, 16, 16, 16, 15, 15, 14, 14, 6, 3, 3, 1, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 21, 21, 21, 71, 71, 201] 201 rigid atoms, others: [45, 43, 47, 7, 8, 9, 10, 11, 12, 13, 14, 44, 46, 39, 15] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 549 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241955 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241955 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241955/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241955 Building REAL300025241956 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241956' /scratch/stefan/7787021/working/building/REAL300025241956 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241956 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241956/0 /scratch/stefan/7787021/working/building/REAL300025241956 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/842 `/scratch/stefan/7787021/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1=CN(C)N=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241956.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241956 none CC(CCNC(=O)CCC1=CN(C)N=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 5, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 62, 69, 69, 74, 75, 75, 75, 151, 151, 201, 201, 201, 201, 201, 53, 62, 24, 52, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 69, 74, 74, 75, 151, 151, 151, 151, 201, 201, 201, 201, 201, 62, 62, 62, 24, 24, 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: 679 number of broken/clashed sets: 137 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241956 none CC(CCNC(=O)CCC1=CN(C)N=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 5, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [27, 26, 25, 21, 21, 6, 21, 3, 1, 1, 1, 1, 1, 1, 1, 27, 28, 28, 29, 29, 63, 103, 201, 201, 201, 201, 201, 27, 27, 27, 27, 27, 27, 25, 25, 21, 6, 6, 3, 3, 1, 2, 2, 2, 1, 28, 28, 28, 63, 63, 201] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 44, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 517 number of broken/clashed sets: 137 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241956 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241956 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241956/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241956 Building REAL300025241957 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241957' /scratch/stefan/7787021/working/building/REAL300025241957 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241957 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241957/0 /scratch/stefan/7787021/working/building/REAL300025241957 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/843 `/scratch/stefan/7787021/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC[NH+]1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241957.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241957 none CC(CCNC(=O)CCC[NH+]1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 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: [45, 45, 45, 48, 48, 60, 60, 60, 67, 60, 68, 68, 68, 68, 68, 68, 45, 45, 32, 45, 13, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 48, 48, 48, 48, 60, 67, 67, 67, 67, 68, 66, 68, 68, 68, 68, 68, 68, 68, 68, 45, 45, 45, 32, 32, 1] 68 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: 310 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: REAL300025241957 none CC(CCNC(=O)CCC[NH+]1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 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: [10, 9, 10, 8, 8, 8, 8, 6, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 21, 28, 68, 68, 68, 68, 68, 10, 10, 10, 10, 10, 10, 10, 10, 8, 8, 8, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 21, 21, 68] 68 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 15, 48, 49, 50, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 51, 52, 53, 54, 55, 56]) total number of confs: 172 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241957 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241957 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241957/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241957 Building REAL300025241958 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241958' /scratch/stefan/7787021/working/building/REAL300025241958 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241958 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241958/0 /scratch/stefan/7787021/working/building/REAL300025241958 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/844 `/scratch/stefan/7787021/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)S1) `REAL300025241958.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241958 none CC1=CC=C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 183, 67, 67, 67, 67, 67, 48, 46, 48, 35, 47, 25, 35, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 183, 183, 67, 67, 67, 67, 67, 48, 48, 48, 48, 47, 47, 47, 25, 25, 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: 808 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: REAL300025241958 none CC1=CC=C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 17, 17, 17, 21, 21, 22, 22, 22, 22, 53, 53, 66, 99, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 6, 6, 17, 21, 21, 21, 21, 22, 22, 22, 22, 22, 22, 22, 66, 66, 201] 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, 46, 47]) total number of confs: 492 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241958 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241958 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241958/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241958 Building REAL300025241959 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241959' /scratch/stefan/7787021/working/building/REAL300025241959 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241959 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241959/0 /scratch/stefan/7787021/working/building/REAL300025241959 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/845 `/scratch/stefan/7787021/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC[NH+]1CCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241959.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241959 none CC(CCNC(=O)CC[NH+]1CCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 39, 40, 40, 40, 58, 58, 58, 58, 58, 58, 58, 58, 39, 39, 27, 39, 12, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 40, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 39, 39, 39, 27, 27, 1] 58 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: 231 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: REAL300025241959 none CC(CCNC(=O)CC[NH+]1CCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 5, 5, 3, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 18, 29, 58, 58, 58, 58, 58, 6, 6, 6, 6, 6, 6, 6, 6, 5, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 58] 58 rigid atoms, others: [45, 43, 8, 9, 10, 11, 12, 13, 14, 15, 48, 49, 44, 46, 50, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54, 55, 56]) total number of confs: 142 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241959 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241959 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241959/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241959 Building REAL300025241960 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241960' /scratch/stefan/7787021/working/building/REAL300025241960 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241960 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241960/0 /scratch/stefan/7787021/working/building/REAL300025241960 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/846 `/scratch/stefan/7787021/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN(CCC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)N=C1) `REAL300025241960.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241960 none CC1=CN(CCC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 194, 193, 132, 132, 132, 118, 115, 83, 59, 83, 46, 59, 30, 46, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 194, 194, 193, 193, 132, 118, 118, 115, 115, 83, 83, 83, 83, 59, 59, 59, 30, 30, 1, 201] 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]) total number of confs: 910 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241960 none CC1=CN(CCC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 7, 10, 10, 10, 16, 17, 24, 24, 28, 28, 55, 55, 70, 109, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 5, 5, 7, 7, 10, 16, 16, 17, 17, 24, 24, 24, 24, 28, 28, 28, 70, 70, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 50, 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, 48, 49]) total number of confs: 536 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241960 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241960 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241960/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241960 Building REAL300025241961 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241961' /scratch/stefan/7787021/working/building/REAL300025241961 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241961 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241961/0 /scratch/stefan/7787021/working/building/REAL300025241961 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/847 `/scratch/stefan/7787021/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241961.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241961 none CCS(=O)(=O)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 3, 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, 7, 7] 0 hydrogens need 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, 126, 126, 126, 115, 94, 86, 73, 86, 50, 73, 25, 49, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 126, 115, 115, 94, 94, 86, 86, 86, 86, 73, 73, 73, 25, 25, 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: 879 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241961 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241961 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241961/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241961 Building REAL300025241962 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241962' /scratch/stefan/7787021/working/building/REAL300025241962 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241962 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241962/0 /scratch/stefan/7787021/working/building/REAL300025241962 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/848 `/scratch/stefan/7787021/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+]1CCCCC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241962.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241962 none CC[N@@H+]1CCCCC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 149, 149, 149, 108, 106, 86, 83, 86, 70, 83, 31, 70, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 149, 108, 108, 106, 106, 86, 86, 86, 86, 83, 83, 83, 31, 31, 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: 733 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: REAL300025241962 none CC[N@@H+]1CCCCC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 13, 15, 17, 17, 21, 21, 25, 25, 47, 81, 201, 201, 201, 201, 201, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 16, 16, 17, 17, 17, 17, 21, 21, 21, 47, 47, 201] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 8, 9, 7, 34, 40, 35, 41, 36, 38, 39, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 448 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241962 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241962/1 /scratch/stefan/7787021/working/building/REAL300025241962 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/849 `/scratch/stefan/7787021/working/3D/849' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+]1CCCCC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241962.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241962/1/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: REAL300025241962 none CC[N@H+]1CCCCC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 147, 147, 147, 103, 101, 82, 80, 82, 68, 80, 30, 68, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 147, 103, 103, 101, 101, 82, 82, 82, 82, 80, 80, 80, 30, 30, 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: 724 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: REAL300025241962 none CC[N@H+]1CCCCC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 13, 15, 16, 16, 21, 21, 25, 25, 47, 80, 201, 201, 201, 201, 201, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 16, 16, 16, 16, 16, 16, 21, 21, 21, 47, 47, 201] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 8, 9, 7, 34, 40, 35, 41, 36, 38, 39, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 446 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241962 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241962 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241962/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241962/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241962 Building REAL300025241963 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241963' /scratch/stefan/7787021/working/building/REAL300025241963 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241963 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241963/0 /scratch/stefan/7787021/working/building/REAL300025241963 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/850 `/scratch/stefan/7787021/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)[C@H]1CCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241963.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241963 none CC(CCNC(=O)[C@H]1CCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [111, 88, 111, 142, 166, 176, 176, 176, 201, 201, 201, 201, 201, 58, 88, 28, 58, 13, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 142, 142, 166, 166, 176, 201, 201, 201, 201, 201, 201, 88, 88, 88, 28, 28, 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: 869 number of broken/clashed sets: 89 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241963 none CC(CCNC(=O)[C@H]1CCCO1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [23, 18, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 23, 32, 32, 41, 41, 77, 115, 201, 201, 201, 201, 201, 23, 23, 23, 23, 18, 18, 12, 12, 5, 1, 1, 1, 1, 1, 1, 32, 32, 32, 77, 77, 201] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45]) total number of confs: 564 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241963 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241963 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241963/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241963 Building REAL300025241964 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241964' /scratch/stefan/7787021/working/building/REAL300025241964 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241964 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241964/0 /scratch/stefan/7787021/working/building/REAL300025241964 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/851 `/scratch/stefan/7787021/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCC(=O)N(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241964.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241964 none CC(CCNC(=O)C1CCC(=O)N(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 85, 94, 100, 105, 106, 106, 106, 201, 201, 201, 201, 201, 201, 201, 62, 85, 22, 61, 12, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 100, 100, 105, 105, 106, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 85, 85, 85, 22, 22, 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: 666 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241964 none CC(CCNC(=O)C1CCC(=O)N(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 15, 18, 18, 25, 25, 64, 107, 201, 201, 201, 201, 201, 15, 15, 15, 15, 12, 12, 11, 11, 7, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 18, 18, 18, 64, 64, 201] 201 rigid atoms, others: [45, 11, 36, 5, 38, 7, 8, 9, 10, 39, 12, 13, 14, 44, 40, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47, 48, 49, 50, 51]) total number of confs: 515 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241964 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241964 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241964/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241964 Building REAL300025241965 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241965' /scratch/stefan/7787021/working/building/REAL300025241965 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241965 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241965/0 /scratch/stefan/7787021/working/building/REAL300025241965 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/852 `/scratch/stefan/7787021/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241965.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241965 none CCOCCOCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 187, 159, 66, 66, 66, 66, 47, 43, 42, 43, 39, 38, 28, 39, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 159, 159, 66, 66, 66, 47, 47, 43, 43, 43, 43, 42, 42, 42, 28, 28, 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: 828 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241965 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241965 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241965/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241965 Building REAL300025241966 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241966' /scratch/stefan/7787021/working/building/REAL300025241966 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241966 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241966/0 /scratch/stefan/7787021/working/building/REAL300025241966 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/853 `/scratch/stefan/7787021/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC(C1CC1)C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241966.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241966 none CC(CCNC(=O)CC(C1CC1)C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [40, 40, 40, 29, 29, 13, 29, 4, 1, 4, 5, 5, 1, 1, 1, 40, 40, 40, 59, 59, 106, 138, 201, 201, 201, 201, 201, 40, 40, 40, 40, 40, 40, 40, 40, 29, 13, 13, 4, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 40, 40, 40, 106, 106, 201] 201 rigid atoms, others: [8, 12, 44, 13, 14, 45, 48, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 49, 50, 51, 52, 53, 54]) total number of confs: 629 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: REAL300025241966 none CC(CCNC(=O)CC(C1CC1)C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [25, 25, 25, 25, 26, 34, 34, 34, 146, 201, 201, 201, 201, 201, 201, 19, 25, 14, 19, 11, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 26, 26, 34, 146, 146, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 25, 25, 25, 14, 14, 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: 791 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: REAL300025241966 none CC(CCNC(=O)CC(C1CC1)C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [38, 38, 38, 26, 26, 10, 26, 3, 1, 1, 1, 1, 3, 5, 5, 38, 38, 38, 57, 57, 104, 136, 201, 201, 201, 201, 201, 38, 38, 38, 38, 38, 38, 38, 38, 26, 10, 10, 3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 38, 38, 38, 104, 104, 201] 201 rigid atoms, others: [43, 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, 38, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 625 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241966 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241966 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241966/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241966 Building REAL300025241967 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241967' /scratch/stefan/7787021/working/building/REAL300025241967 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241967 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241967/0 /scratch/stefan/7787021/working/building/REAL300025241967 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/854 `/scratch/stefan/7787021/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)C1CC1) `REAL300025241967.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241967 none CC(CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)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.3', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 13, 13, 13, 20, 27, 31, 31, 32, 32, 36, 36, 73, 111, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 2, 4, 4, 13, 20, 20, 27, 27, 31, 31, 31, 31, 32, 32, 32, 73, 73, 201, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 46, 47, 48, 49, 50, 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, 44, 45]) total number of confs: 566 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: REAL300025241967 none CC(CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)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.3', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 86, 86, 86, 86, 75, 66, 65, 66, 49, 65, 25, 48, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 86, 86, 86, 75, 75, 66, 66, 66, 66, 65, 65, 65, 25, 25, 1, 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]) total number of confs: 857 number of broken/clashed sets: 154 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241967 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241967 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241967/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241967 Building REAL300025241968 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241968' /scratch/stefan/7787021/working/building/REAL300025241968 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241968 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241968/0 /scratch/stefan/7787021/working/building/REAL300025241968 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/855 `/scratch/stefan/7787021/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CC2CCC1CC2)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241968.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241968 none CC(CCNC(=O)C1CC2CCC1CC2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [141, 120, 141, 172, 186, 194, 194, 194, 201, 201, 201, 201, 201, 201, 201, 88, 120, 30, 88, 13, 1, 1, 1, 1, 1, 1, 1, 141, 141, 141, 141, 172, 172, 186, 186, 194, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 120, 120, 120, 30, 30, 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: 791 number of broken/clashed sets: 93 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241968 none CC(CCNC(=O)C1CC2CCC1CC2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [24, 14, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 24, 29, 29, 39, 39, 74, 115, 201, 201, 201, 201, 201, 24, 24, 24, 24, 16, 16, 12, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 74, 74, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 49, 50, 51, 52, 53, 54]) total number of confs: 546 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241968 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241968 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241968/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241968 Building REAL300025241969 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241969' /scratch/stefan/7787021/working/building/REAL300025241969 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241969 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241969/0 /scratch/stefan/7787021/working/building/REAL300025241969 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/856 `/scratch/stefan/7787021/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)C(C)C) `REAL300025241969.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241969 none CCCCC(C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)C(C)C 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.3', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 200, 133, 133, 133, 103, 103, 71, 57, 71, 43, 57, 32, 43, 12, 1, 1, 1, 1, 1, 1, 1, 200, 201, 195, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 133, 103, 103, 103, 103, 71, 71, 71, 71, 57, 57, 57, 32, 32, 1, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [51, 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, 49, 50, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 972 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241969 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241969 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241969/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241969 Building REAL300025241970 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241970' /scratch/stefan/7787021/working/building/REAL300025241970 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241970 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241970/0 /scratch/stefan/7787021/working/building/REAL300025241970 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/857 `/scratch/stefan/7787021/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)O1) `REAL300025241970.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241970 none CC1=NC=C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 83, 83, 83, 83, 83, 56, 54, 56, 41, 55, 30, 41, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 194, 194, 83, 83, 83, 83, 83, 56, 56, 56, 56, 55, 55, 55, 30, 30, 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: 865 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: REAL300025241970 none CC1=NC=C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 16, 16, 16, 20, 20, 22, 22, 22, 22, 53, 53, 69, 100, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 6, 6, 16, 20, 20, 20, 20, 22, 22, 22, 22, 22, 22, 22, 69, 69, 201] 201 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, 45, 46]) total number of confs: 519 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241970 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241970 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241970/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241970 Building REAL300025241971 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241971' /scratch/stefan/7787021/working/building/REAL300025241971 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241971 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241971/0 /scratch/stefan/7787021/working/building/REAL300025241971 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/858 `/scratch/stefan/7787021/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1([NH+](C)C)CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241971.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241971 none CC(CCNC(=O)C1([NH+](C)C)CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [129, 109, 129, 179, 179, 198, 198, 198, 201, 201, 201, 201, 201, 201, 201, 88, 109, 32, 88, 13, 1, 1, 1, 1, 1, 1, 1, 129, 129, 129, 129, 179, 179, 179, 179, 198, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 109, 109, 109, 32, 32, 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: 819 number of broken/clashed sets: 105 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241971 none CC(CCNC(=O)C1([NH+](C)C)CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 8, 10, 4, 4, 1, 4, 1, 1, 2, 2, 2, 1, 1, 1, 15, 18, 18, 27, 27, 64, 116, 201, 201, 201, 201, 201, 15, 15, 15, 15, 10, 10, 10, 10, 4, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 64, 64, 201] 201 rigid atoms, others: [5, 7, 8, 44, 42, 43, 12, 13, 14, 45, 46, 47] set([0, 1, 2, 3, 4, 6, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50, 51, 52, 53]) total number of confs: 514 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241971 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241971 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241971/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241971 Building REAL300025241972 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241972' /scratch/stefan/7787021/working/building/REAL300025241972 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241972 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241972/0 /scratch/stefan/7787021/working/building/REAL300025241972 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/859 `/scratch/stefan/7787021/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1=CSC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241972.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241972 none CC(CCNC(=O)CCC1=CSC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 1, 1, 14, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [31, 31, 31, 33, 39, 40, 40, 40, 110, 111, 201, 201, 201, 201, 31, 31, 17, 31, 9, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 33, 33, 39, 39, 40, 110, 110, 111, 111, 201, 201, 201, 31, 31, 31, 17, 17, 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: 637 number of broken/clashed sets: 143 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241972 none CC(CCNC(=O)CCC1=CSC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 1, 1, 14, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [42, 40, 33, 23, 23, 6, 23, 2, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 81, 122, 201, 201, 201, 201, 201, 42, 42, 42, 42, 40, 40, 33, 33, 23, 6, 6, 2, 2, 1, 1, 1, 42, 42, 42, 81, 81, 201] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46, 47]) total number of confs: 580 number of broken/clashed sets: 143 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241972 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241972 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241972/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241972 Building REAL300025241973 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241973' /scratch/stefan/7787021/working/building/REAL300025241973 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241973 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241973/0 /scratch/stefan/7787021/working/building/REAL300025241973 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/860 `/scratch/stefan/7787021/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=C(F)C(F)=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241973.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241973 none CC(CCNC(=O)C1=CC=C(F)C(F)=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 15, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [72, 61, 72, 73, 74, 74, 74, 74, 201, 201, 201, 201, 201, 201, 201, 53, 61, 24, 52, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 73, 73, 74, 74, 74, 201, 201, 201, 61, 61, 61, 24, 24, 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: 453 number of broken/clashed sets: 79 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241973 none CC(CCNC(=O)C1=CC=C(F)C(F)=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 15, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [13, 9, 10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 13, 19, 19, 23, 23, 48, 85, 201, 201, 201, 201, 201, 13, 13, 13, 13, 10, 10, 10, 10, 5, 1, 1, 1, 19, 19, 19, 48, 48, 201] 201 rigid atoms, others: [36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44]) total number of confs: 455 number of broken/clashed sets: 79 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241973 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241973 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241973/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241973 Building REAL300025241974 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241974' /scratch/stefan/7787021/working/building/REAL300025241974 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241974 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241974/0 /scratch/stefan/7787021/working/building/REAL300025241974 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/861 `/scratch/stefan/7787021/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC(F)=CC=C1F)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241974.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241974 none CC(CCNC(=O)C1=CC(F)=CC=C1F)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 1, 15, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [125, 105, 125, 153, 171, 187, 187, 187, 201, 201, 201, 201, 201, 201, 201, 69, 105, 27, 68, 13, 1, 1, 1, 1, 1, 1, 1, 125, 125, 125, 125, 153, 153, 171, 171, 187, 201, 201, 201, 105, 105, 105, 27, 27, 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: 786 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: REAL300025241974 none CC(CCNC(=O)C1=CC(F)=CC=C1F)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 1, 15, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [19, 14, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 19, 29, 29, 37, 37, 70, 105, 201, 201, 201, 201, 201, 19, 19, 19, 19, 15, 15, 13, 13, 4, 1, 1, 1, 29, 29, 29, 70, 70, 201] 201 rigid atoms, others: [36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44]) total number of confs: 528 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241974 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241974 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241974/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241974 Building REAL300025241975 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241975' /scratch/stefan/7787021/working/building/REAL300025241975 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241975 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241975/0 /scratch/stefan/7787021/working/building/REAL300025241975 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/862 `/scratch/stefan/7787021/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(OCC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=NO1) `REAL300025241975.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241975 none CC1=CC(OCC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 113, 113, 113, 91, 91, 64, 59, 64, 45, 59, 28, 45, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 200, 200, 113, 91, 91, 91, 91, 64, 64, 64, 64, 59, 59, 59, 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: 849 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241975 none CC1=CC(OCC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 5, 14, 14, 14, 19, 19, 26, 26, 29, 29, 55, 55, 73, 111, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 5, 5, 14, 19, 19, 19, 19, 26, 26, 26, 26, 29, 29, 29, 73, 73, 201] 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: 537 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241975 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241975 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241975/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241975 Building REAL300025241976 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241976' /scratch/stefan/7787021/working/building/REAL300025241976 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241976 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241976/0 /scratch/stefan/7787021/working/building/REAL300025241976 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/863 `/scratch/stefan/7787021/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C(C)(C)C(N)=O)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241976.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241976 none CC(CCNC(=O)C(C)(C)C(N)=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 59, 71, 88, 105, 110, 110, 110, 188, 188, 188, 201, 201, 38, 59, 22, 37, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 88, 88, 105, 105, 110, 188, 188, 188, 188, 188, 188, 201, 201, 59, 59, 59, 22, 22, 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: 950 number of broken/clashed sets: 98 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241976 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241976 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241976/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241976 Building REAL300025241977 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241977' /scratch/stefan/7787021/working/building/REAL300025241977 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241977 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241977/0 /scratch/stefan/7787021/working/building/REAL300025241977 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/864 `/scratch/stefan/7787021/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)[NH+](C)C) `REAL300025241977.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241977 none CC(C)[C@@H](C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)[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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [161, 201, 201, 160, 201, 160, 160, 125, 124, 91, 88, 91, 72, 88, 28, 71, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 160, 125, 125, 124, 124, 91, 91, 91, 91, 88, 88, 88, 28, 28, 1, 201, 201, 201, 201, 201, 201] 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, 54, 55]) total number of confs: 1161 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241977 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241977 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241977/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241977 Building REAL300025241978 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241978' /scratch/stefan/7787021/working/building/REAL300025241978 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241978 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241978/0 /scratch/stefan/7787021/working/building/REAL300025241978 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/865 `/scratch/stefan/7787021/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)N(C)C=N1) `REAL300025241978.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241978 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 106, 92, 79, 70, 79, 49, 70, 26, 48, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 113, 106, 106, 92, 92, 79, 79, 79, 79, 70, 70, 70, 26, 26, 1, 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]) total number of confs: 605 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241978 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 16, 19, 19, 23, 23, 32, 32, 65, 102, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 7, 15, 15, 17, 17, 19, 19, 19, 19, 23, 23, 23, 65, 65, 201, 2, 2, 2, 1] 201 rigid atoms, others: [0, 1, 2, 3, 47, 22, 23, 24, 25] set([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, 45, 46]) total number of confs: 525 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241978 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241978 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241978/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241978 Building REAL300025241979 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241979' /scratch/stefan/7787021/working/building/REAL300025241979 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241979 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241979/0 /scratch/stefan/7787021/working/building/REAL300025241979 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/866 `/scratch/stefan/7787021/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1=CN=CS1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241979.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241979 none CC(CCNC(=O)CC1=CN=CS1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 5, 1, 1, 8, 1, 14, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [54, 49, 54, 54, 55, 55, 55, 55, 156, 201, 201, 201, 201, 40, 49, 24, 39, 13, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 54, 55, 55, 55, 156, 156, 201, 201, 49, 49, 49, 24, 24, 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: 694 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241979 none CC(CCNC(=O)CC1=CN=CS1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 5, 1, 1, 8, 1, 14, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 17, 17, 13, 13, 3, 13, 1, 1, 1, 1, 1, 1, 18, 19, 19, 25, 25, 61, 102, 201, 201, 201, 201, 201, 18, 18, 18, 18, 17, 17, 17, 17, 13, 3, 3, 1, 1, 19, 19, 19, 61, 61, 201] 201 rigid atoms, others: [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, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 493 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241979 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241979 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241979/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241979 Building REAL300025241980 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241980' /scratch/stefan/7787021/working/building/REAL300025241980 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241980 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241980/0 /scratch/stefan/7787021/working/building/REAL300025241980 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/867 `/scratch/stefan/7787021/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC(=O)NN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241980.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241980 none CC(CCNC(=O)C1=CC(=O)NN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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: [65, 56, 65, 68, 76, 78, 78, 78, 201, 201, 201, 201, 201, 201, 45, 56, 22, 45, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 68, 68, 76, 76, 78, 201, 201, 201, 56, 56, 56, 22, 22, 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: 481 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241980 none CC(CCNC(=O)C1=CC(=O)NN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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: [14, 11, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 14, 18, 18, 28, 28, 58, 93, 201, 201, 201, 201, 201, 14, 14, 14, 14, 11, 11, 9, 9, 5, 1, 1, 1, 18, 18, 18, 58, 58, 201] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 486 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241980 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241980 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241980/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241980 Building REAL300025241981 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241981' /scratch/stefan/7787021/working/building/REAL300025241981 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241981 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241981/0 /scratch/stefan/7787021/working/building/REAL300025241981 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/868 `/scratch/stefan/7787021/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)NC(=O)N1) `REAL300025241981.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241981 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 101, 101, 101, 101, 96, 87, 77, 87, 60, 77, 26, 60, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 101, 101, 101, 96, 96, 87, 87, 87, 87, 77, 77, 77, 26, 26, 1, 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]) total number of confs: 561 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: REAL300025241981 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 8, 8, 8, 11, 12, 17, 17, 21, 21, 28, 28, 62, 102, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 8, 11, 11, 13, 13, 17, 17, 17, 17, 21, 21, 21, 62, 62, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 45, 22, 23, 24, 25] set([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: 507 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241981 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241981 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241981/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241981 Building REAL300025241982 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241982' /scratch/stefan/7787021/working/building/REAL300025241982 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241982 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241982/0 /scratch/stefan/7787021/working/building/REAL300025241982 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/869 `/scratch/stefan/7787021/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NN(C)C=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241982.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241982 none CCC1=NN(C)C=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 153, 153, 153, 153, 153, 153, 132, 132, 132, 126, 120, 114, 110, 114, 88, 110, 30, 88, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 153, 153, 153, 153, 132, 126, 126, 120, 120, 114, 114, 114, 114, 110, 110, 110, 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: 789 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: REAL300025241982 none CCC1=NN(C)C=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 10, 10, 14, 14, 14, 14, 18, 18, 44, 70, 153, 153, 153, 153, 153, 5, 5, 5, 4, 4, 2, 2, 2, 1, 3, 10, 10, 11, 11, 14, 14, 14, 14, 14, 14, 14, 44, 44, 153] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 35] set([0, 9, 10, 11, 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, 45, 46, 47, 48, 49, 50]) total number of confs: 388 number of broken/clashed sets: 123 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241982 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241982 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241982/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241982 Building REAL300025241983 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241983' /scratch/stefan/7787021/working/building/REAL300025241983 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241983 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241983/0 /scratch/stefan/7787021/working/building/REAL300025241983 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/870 `/scratch/stefan/7787021/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1(C2CC2)CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241983.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241983 none CC(CCNC(=O)C1(C2CC2)CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [31, 26, 22, 15, 15, 8, 15, 1, 1, 1, 1, 8, 8, 31, 31, 31, 37, 37, 68, 105, 201, 201, 201, 201, 201, 31, 31, 31, 31, 26, 26, 22, 22, 15, 1, 1, 1, 1, 1, 8, 8, 8, 8, 31, 31, 31, 68, 68, 201] 201 rigid atoms, others: [34, 35, 36, 37, 38, 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, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 519 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: REAL300025241983 none CC(CCNC(=O)C1(C2CC2)CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [56, 56, 56, 63, 69, 71, 71, 71, 133, 201, 201, 133, 133, 48, 56, 25, 48, 13, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 63, 63, 69, 69, 71, 201, 201, 201, 201, 201, 133, 133, 133, 133, 56, 56, 56, 25, 25, 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: 738 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: REAL300025241983 none CC(CCNC(=O)C1(C2CC2)CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [14, 10, 8, 4, 4, 1, 4, 1, 1, 8, 8, 1, 1, 14, 14, 14, 18, 18, 36, 57, 133, 133, 133, 133, 133, 14, 14, 14, 14, 10, 10, 8, 8, 4, 8, 8, 8, 8, 8, 1, 1, 1, 1, 14, 14, 14, 36, 36, 133] 201 rigid atoms, others: [5, 39, 8, 41, 42, 11, 12, 40, 7] set([0, 1, 2, 3, 4, 6, 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]) total number of confs: 326 number of broken/clashed sets: 113 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241983 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241983 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241983/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241983 Building REAL300025241984 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241984' /scratch/stefan/7787021/working/building/REAL300025241984 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241984 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241984/0 /scratch/stefan/7787021/working/building/REAL300025241984 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/871 `/scratch/stefan/7787021/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025241984.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241984 none COC1CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 123, 123, 123, 105, 105, 63, 62, 63, 51, 63, 30, 51, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 123, 105, 105, 105, 105, 63, 63, 63, 63, 63, 63, 63, 30, 30, 1, 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]) total number of confs: 785 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: REAL300025241984 none COC1CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 11, 11, 18, 18, 18, 18, 36, 36, 52, 87, 201, 201, 201, 201, 201, 1, 3, 3, 3, 1, 1, 1, 1, 8, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 52, 52, 201, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 47, 48, 24, 28, 29, 30, 31] set([0, 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: 454 number of broken/clashed sets: 110 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241984 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241984 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241984/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241984 Building REAL300025241985 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241985' /scratch/stefan/7787021/working/building/REAL300025241985 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241985 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241985/0 /scratch/stefan/7787021/working/building/REAL300025241985 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/872 `/scratch/stefan/7787021/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)[C@H]1CCCC(=O)N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241985.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241985 none CC(CCNC(=O)[C@H]1CCCC(=O)N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 98, 108, 124, 144, 156, 156, 156, 201, 201, 201, 201, 201, 201, 201, 68, 98, 28, 68, 13, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 124, 124, 144, 144, 156, 201, 201, 201, 201, 201, 201, 201, 98, 98, 98, 28, 28, 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: 774 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241985 none CC(CCNC(=O)[C@H]1CCCC(=O)N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 17, 20, 20, 30, 30, 67, 103, 201, 201, 201, 201, 201, 17, 17, 17, 17, 15, 15, 13, 13, 9, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 67, 67, 201] 201 rigid atoms, others: [36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47, 48]) total number of confs: 505 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241985 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241985 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241985/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241985 Building REAL300025241986 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241986' /scratch/stefan/7787021/working/building/REAL300025241986 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241986 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241986/0 /scratch/stefan/7787021/working/building/REAL300025241986 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/873 `/scratch/stefan/7787021/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1CCN(C)C1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241986.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241986 none CC(CCNC(=O)CC1CCN(C)C1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 88, 113, 124, 124, 124, 189, 201, 201, 201, 201, 201, 201, 57, 69, 25, 56, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 88, 88, 113, 113, 124, 189, 189, 201, 201, 201, 201, 201, 201, 201, 201, 69, 69, 69, 25, 25, 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: 869 number of broken/clashed sets: 111 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241986 none CC(CCNC(=O)CC1CCN(C)C1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 22, 11, 11, 5, 11, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 35, 35, 74, 111, 201, 201, 201, 201, 201, 28, 28, 28, 28, 24, 24, 22, 22, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 74, 74, 201] 201 rigid atoms, others: [45, 11, 38, 7, 8, 9, 10, 39, 12, 13, 14, 44, 40, 43, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 46, 47, 48, 49, 50, 51]) total number of confs: 564 number of broken/clashed sets: 111 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241986 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241986 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241986/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241986 Building REAL300025241987 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241987' /scratch/stefan/7787021/working/building/REAL300025241987 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241987 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241987/0 /scratch/stefan/7787021/working/building/REAL300025241987 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/874 `/scratch/stefan/7787021/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CCCC1) `REAL300025241987.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241987 none COCC1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CCCC1 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.3', 'C.2', '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, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 135, 135, 135, 114, 103, 82, 64, 82, 43, 64, 23, 43, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 135, 114, 114, 103, 103, 82, 82, 82, 82, 64, 64, 64, 23, 23, 1, 201, 201, 201, 201, 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: 809 number of broken/clashed sets: 107 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241987 none COCC1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CCCC1 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.3', 'C.2', '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, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 1, 1, 3, 3, 3, 9, 11, 16, 16, 22, 22, 32, 32, 66, 102, 201, 201, 201, 201, 201, 1, 1, 1, 1, 5, 5, 5, 3, 3, 3, 9, 9, 11, 11, 16, 16, 16, 16, 22, 22, 22, 66, 66, 201, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 47, 48, 49, 50, 51, 52, 53, 54, 23, 24, 25, 26] set([0, 1, 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: 544 number of broken/clashed sets: 107 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241987 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241987 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241987/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241987 Building REAL300025241988 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241988' /scratch/stefan/7787021/working/building/REAL300025241988 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241988 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241988/0 /scratch/stefan/7787021/working/building/REAL300025241988 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/875 `/scratch/stefan/7787021/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=NN2CCCC2=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241988.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241988 none CC(CCNC(=O)C1=NN2CCCC2=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 8, 8, 5, 5, 5, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [126, 110, 126, 165, 182, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 62, 110, 27, 62, 13, 1, 1, 1, 1, 1, 1, 1, 126, 126, 126, 126, 165, 165, 182, 182, 201, 201, 201, 201, 201, 201, 201, 201, 110, 110, 110, 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: 835 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241988 none CC(CCNC(=O)C1=NN2CCCC2=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 8, 8, 5, 5, 5, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [13, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 19, 19, 33, 33, 67, 104, 201, 201, 201, 201, 201, 13, 13, 13, 13, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 67, 67, 201] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 40, 3, 41, 36, 38, 42, 39, 37] set([0, 1, 2, 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]) total number of confs: 510 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241988 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241988 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241988/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241988 Building REAL300025241989 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241989' /scratch/stefan/7787021/working/building/REAL300025241989 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241989 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241989/0 /scratch/stefan/7787021/working/building/REAL300025241989 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/876 `/scratch/stefan/7787021/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)SC=N1) `REAL300025241989.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241989 none CCC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)SC=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 176, 176, 173, 159, 126, 109, 126, 74, 109, 30, 74, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 176, 173, 173, 159, 159, 126, 126, 126, 126, 109, 109, 109, 30, 30, 1, 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]) total number of confs: 748 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241989 none CCC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)SC=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 4, 11, 11, 16, 16, 19, 19, 26, 26, 59, 93, 201, 201, 201, 201, 201, 1, 1, 1, 4, 4, 4, 3, 3, 4, 11, 11, 12, 12, 16, 16, 16, 16, 19, 19, 19, 59, 59, 201, 1] 201 rigid atoms, others: [1, 2, 3, 4, 46, 23, 24, 25] set([0, 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: 500 number of broken/clashed sets: 113 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241989 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241989 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241989/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241989 Building REAL300025241990 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241990' /scratch/stefan/7787021/working/building/REAL300025241990 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241990 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241990/0 /scratch/stefan/7787021/working/building/REAL300025241990 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/877 `/scratch/stefan/7787021/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=C2CCCN2N=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241990.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241990 none CC(CCNC(=O)C1=C2CCCN2N=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [145, 121, 145, 165, 171, 173, 173, 173, 201, 201, 201, 201, 201, 201, 201, 98, 121, 31, 98, 13, 1, 1, 1, 1, 1, 1, 1, 145, 145, 145, 145, 165, 165, 171, 171, 173, 201, 201, 201, 201, 201, 201, 201, 121, 121, 121, 31, 31, 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: 710 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: REAL300025241990 none CC(CCNC(=O)C1=C2CCCN2N=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [17, 11, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 23, 23, 29, 29, 65, 106, 201, 201, 201, 201, 201, 17, 17, 17, 17, 14, 14, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 65, 65, 201] 201 rigid atoms, others: [36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47, 48]) total number of confs: 514 number of broken/clashed sets: 110 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241990 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241990 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241990/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241990 Building REAL300025241991 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241991' /scratch/stefan/7787021/working/building/REAL300025241991 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241991 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241991/0 /scratch/stefan/7787021/working/building/REAL300025241991 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/878 `/scratch/stefan/7787021/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCC(F)(F)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241991.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241991 none CC(CCNC(=O)C1CCC(F)(F)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [104, 96, 104, 112, 117, 117, 117, 117, 201, 201, 201, 201, 201, 201, 71, 96, 26, 70, 12, 1, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 112, 112, 117, 117, 117, 201, 201, 201, 201, 201, 201, 201, 96, 96, 96, 26, 26, 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: 698 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: REAL300025241991 none CC(CCNC(=O)C1CCC(F)(F)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 13, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 16, 18, 18, 27, 27, 69, 117, 201, 201, 201, 201, 201, 16, 16, 16, 16, 13, 13, 12, 12, 8, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 69, 69, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 39, 12, 13, 11, 40, 41, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47]) total number of confs: 520 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241991 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241991 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241991/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241991 Building REAL300025241992 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241992' /scratch/stefan/7787021/working/building/REAL300025241992 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241992 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241992/0 /scratch/stefan/7787021/working/building/REAL300025241992 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/879 `/scratch/stefan/7787021/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1(F)CCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241992.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241992 none CC(CCNC(=O)C1(F)CCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 7] 0 hydrogens 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, 86, 99, 108, 119, 121, 121, 121, 201, 201, 201, 201, 201, 201, 65, 86, 28, 64, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 99, 108, 108, 119, 119, 121, 201, 201, 201, 201, 201, 201, 201, 201, 86, 86, 86, 28, 28, 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: 745 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: REAL300025241992 none CC(CCNC(=O)C1(F)CCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 7] 0 hydrogens 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, 15, 10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 20, 26, 26, 35, 35, 74, 117, 201, 201, 201, 201, 201, 20, 20, 20, 20, 15, 15, 10, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 74, 74, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46, 47, 48]) total number of confs: 556 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241992 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241992 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241992/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241992 Building REAL300025241993 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241993' /scratch/stefan/7787021/working/building/REAL300025241993 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241993 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241993/0 /scratch/stefan/7787021/working/building/REAL300025241993 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/880 `/scratch/stefan/7787021/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1=CNC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241993.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241993 none CC(CCNC(=O)CCC1=CNC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 53, 68, 90, 103, 135, 135, 135, 201, 201, 201, 201, 201, 201, 53, 53, 31, 52, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 90, 90, 103, 103, 135, 201, 201, 201, 201, 201, 201, 201, 53, 53, 53, 31, 31, 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: 876 number of broken/clashed sets: 147 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241993 none CC(CCNC(=O)CCC1=CNC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 23, 14, 14, 9, 14, 5, 1, 1, 1, 1, 1, 1, 30, 33, 33, 35, 35, 74, 110, 201, 201, 201, 201, 201, 30, 30, 30, 30, 23, 23, 23, 23, 14, 9, 9, 5, 5, 1, 1, 1, 33, 33, 33, 74, 74, 201] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46, 47]) total number of confs: 577 number of broken/clashed sets: 147 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241993 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241993/1 /scratch/stefan/7787021/working/building/REAL300025241993 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/881 `/scratch/stefan/7787021/working/3D/881' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1=CN=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241993.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241993/1/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: REAL300025241993 none CC(CCNC(=O)CCC1=CN=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 56, 69, 79, 79, 79, 160, 182, 201, 201, 201, 201, 45, 54, 20, 45, 12, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 56, 56, 69, 69, 79, 160, 160, 182, 182, 201, 201, 201, 54, 54, 54, 20, 20, 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: 829 number of broken/clashed sets: 116 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241993 none CC(CCNC(=O)CCC1=CN=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 19, 19, 6, 19, 3, 1, 1, 1, 1, 1, 1, 31, 31, 31, 37, 37, 68, 107, 201, 201, 201, 201, 201, 31, 31, 31, 31, 30, 30, 25, 25, 19, 6, 6, 3, 3, 1, 1, 1, 31, 31, 31, 68, 68, 201] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46, 47]) total number of confs: 538 number of broken/clashed sets: 116 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241993 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241993 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241993/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241993/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241993 Building REAL300025241994 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241994' /scratch/stefan/7787021/working/building/REAL300025241994 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241994 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241994/0 /scratch/stefan/7787021/working/building/REAL300025241994 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/882 `/scratch/stefan/7787021/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCN1C=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241994.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241994 none C=CCN1C=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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: [1, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 149, 149, 149, 149, 88, 88, 88, 88, 88, 59, 58, 59, 40, 59, 29, 40, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 149, 149, 149, 88, 88, 88, 88, 88, 59, 59, 59, 59, 59, 59, 59, 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: 811 number of broken/clashed sets: 93 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241994 none C=CCN1C=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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: [1, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 7, 19, 19, 32, 54, 149, 149, 149, 149, 149, 10, 10, 10, 3, 3, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 32, 32, 149] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34] 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 353 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241994 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241994 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241994/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241994 Building REAL300025241995 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241995' /scratch/stefan/7787021/working/building/REAL300025241995 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025241995 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241995/0 /scratch/stefan/7787021/working/building/REAL300025241995 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/883 `/scratch/stefan/7787021/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C[N@H+](C)C1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241995.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241995 none CC(CCNC(=O)C[N@H+](C)C1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 126, 154, 168, 168, 186, 186, 186, 201, 201, 201, 201, 201, 201, 201, 114, 126, 36, 114, 13, 1, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 168, 168, 168, 168, 186, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 126, 126, 126, 36, 36, 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: 791 number of broken/clashed sets: 153 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241995 none CC(CCNC(=O)C[N@H+](C)C1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 20, 25, 12, 12, 5, 12, 2, 1, 2, 2, 1, 1, 1, 1, 25, 26, 26, 30, 30, 82, 126, 201, 201, 201, 201, 201, 25, 25, 25, 25, 25, 25, 25, 25, 12, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 82, 82, 201] 201 rigid atoms, others: [45, 43, 8, 41, 42, 11, 12, 13, 14, 44, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 51, 52, 53]) total number of confs: 590 number of broken/clashed sets: 153 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241995 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025241995/1 /scratch/stefan/7787021/working/building/REAL300025241995 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/884 `/scratch/stefan/7787021/working/3D/884' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C[N@@H+](C)C1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241995.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025241995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241995/1/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: REAL300025241995 none CC(CCNC(=O)C[N@@H+](C)C1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 86, 117, 140, 140, 175, 175, 175, 201, 201, 201, 201, 201, 201, 201, 81, 86, 35, 80, 13, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 140, 140, 140, 140, 175, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 86, 86, 86, 35, 35, 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: 866 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241995 none CC(CCNC(=O)C[N@@H+](C)C1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 26, 31, 15, 15, 6, 15, 3, 1, 3, 3, 1, 1, 1, 1, 32, 36, 36, 38, 38, 81, 122, 201, 201, 201, 201, 201, 32, 32, 32, 32, 31, 31, 31, 31, 15, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 81, 81, 201] 201 rigid atoms, others: [45, 43, 8, 41, 42, 11, 12, 13, 14, 44, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 51, 52, 53]) total number of confs: 590 number of broken/clashed sets: 156 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241995 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241995 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241995/0.* 1: /scratch/stefan/7787021/working/building/REAL300025241995/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241995 Building REAL300025241996 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241996' /scratch/stefan/7787021/working/building/REAL300025241996 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241996 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241996/0 /scratch/stefan/7787021/working/building/REAL300025241996 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/885 `/scratch/stefan/7787021/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=NN2CCOC2=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241996.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241996 none CC(CCNC(=O)C1=NN2CCOC2=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 8, 8, 5, 5, 12, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [130, 115, 130, 167, 184, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 66, 115, 27, 66, 13, 1, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 167, 167, 184, 184, 201, 201, 201, 201, 201, 201, 115, 115, 115, 27, 27, 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: 813 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: REAL300025241996 none CC(CCNC(=O)C1=NN2CCOC2=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 8, 8, 5, 5, 12, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [15, 10, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 15, 21, 21, 34, 34, 69, 106, 201, 201, 201, 201, 201, 15, 15, 15, 15, 10, 10, 8, 8, 3, 1, 1, 1, 1, 1, 21, 21, 21, 69, 69, 201] 201 rigid atoms, others: [36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46]) total number of confs: 517 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241996 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241996 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241996/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241996 Building REAL300025241997 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241997' /scratch/stefan/7787021/working/building/REAL300025241997 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241997 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241997/0 /scratch/stefan/7787021/working/building/REAL300025241997 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/886 `/scratch/stefan/7787021/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=N1) `REAL300025241997.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241997 none CCC1=CC=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 132, 132, 132, 132, 132, 131, 131, 131, 106, 106, 83, 68, 83, 53, 69, 35, 53, 12, 1, 1, 1, 1, 1, 1, 1, 132, 201, 201, 201, 201, 201, 132, 132, 132, 131, 106, 106, 106, 106, 83, 83, 83, 83, 69, 69, 69, 35, 35, 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: 981 number of broken/clashed sets: 79 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241997 none CCC1=CC=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 15, 15, 28, 28, 36, 58, 132, 132, 132, 132, 132, 1, 6, 6, 6, 6, 6, 1, 1, 1, 3, 8, 8, 8, 8, 12, 12, 12, 12, 15, 15, 15, 36, 36, 132] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 319 number of broken/clashed sets: 79 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241997 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241997 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241997/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241997 Building REAL300025241998 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241998' /scratch/stefan/7787021/working/building/REAL300025241998 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241998 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241998/0 /scratch/stefan/7787021/working/building/REAL300025241998 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/887 `/scratch/stefan/7787021/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C=C1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241998.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241998 none CC1=NN(C)C=C1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 159, 47, 47, 47, 47, 47, 35, 35, 35, 23, 35, 18, 23, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 159, 159, 47, 47, 47, 47, 47, 35, 35, 35, 35, 35, 35, 35, 18, 18, 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: 714 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241998 none CC1=NN(C)C=C1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 21, 21, 21, 25, 25, 25, 25, 25, 25, 56, 56, 66, 98, 201, 201, 201, 201, 201, 2, 2, 2, 2, 2, 2, 1, 6, 6, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 66, 66, 201] 201 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, 49, 50]) total number of confs: 486 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241998 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241998 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241998/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241998 Building REAL300025241999 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025241999' /scratch/stefan/7787021/working/building/REAL300025241999 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025241999 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025241999/0 /scratch/stefan/7787021/working/building/REAL300025241999 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/888 `/scratch/stefan/7787021/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C(C)(C)C1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025241999.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025241999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025241999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025241999 none CC(CCNC(=O)C(C)(C)C1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 68, 72, 87, 97, 107, 107, 107, 198, 198, 198, 201, 201, 201, 201, 51, 68, 27, 50, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 87, 87, 97, 97, 107, 198, 198, 198, 198, 198, 198, 201, 201, 201, 201, 201, 201, 201, 201, 201, 68, 68, 68, 27, 27, 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: 912 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: REAL300025241999 none CC(CCNC(=O)C(C)(C)C1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 14, 15, 5, 5, 3, 5, 1, 3, 3, 1, 1, 1, 1, 1, 21, 22, 22, 33, 33, 67, 103, 201, 201, 201, 201, 201, 21, 21, 21, 21, 17, 17, 15, 15, 5, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 67, 67, 201] 201 rigid atoms, others: [43, 7, 44, 10, 11, 12, 13, 14, 45, 48, 49, 50, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56]) total number of confs: 537 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025241999 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025241999 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025241999/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025241999 Building REAL300025242000 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242000' /scratch/stefan/7787021/working/building/REAL300025242000 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242000 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242000/0 /scratch/stefan/7787021/working/building/REAL300025242000 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/889 `/scratch/stefan/7787021/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1(C)CCCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242000.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242000 none CC(CCNC(=O)C1(C)CCCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 103, 123, 147, 163, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 62, 103, 26, 61, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 147, 147, 163, 163, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 103, 103, 26, 26, 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: 798 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: REAL300025242000 none CC(CCNC(=O)C1(C)CCCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 16, 27, 27, 42, 42, 73, 110, 201, 201, 201, 201, 201, 16, 16, 16, 16, 11, 11, 8, 8, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 73, 73, 201] 201 rigid atoms, others: [45, 11, 5, 7, 8, 9, 10, 39, 12, 13, 14, 44, 48, 40, 50, 46, 43, 41, 49, 47, 42] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 51, 52, 53, 54, 55, 56]) total number of confs: 544 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242000 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242000 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242000/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242000 Building REAL300025242001 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242001' /scratch/stefan/7787021/working/building/REAL300025242001 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242001 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242001/0 /scratch/stefan/7787021/working/building/REAL300025242001 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/890 `/scratch/stefan/7787021/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=C(F)C=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242001.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242001 none CC(CCNC(=O)C1=CC=C(F)C=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 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: [127, 108, 127, 159, 179, 201, 201, 201, 201, 201, 201, 201, 201, 201, 68, 108, 28, 68, 13, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 159, 159, 179, 179, 201, 201, 201, 201, 108, 108, 108, 28, 28, 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: 826 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: REAL300025242001 none CC(CCNC(=O)C1=CC=C(F)C=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 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, 9, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 26, 26, 38, 38, 68, 106, 201, 201, 201, 201, 201, 17, 17, 17, 17, 10, 10, 7, 7, 1, 1, 1, 1, 26, 26, 26, 68, 68, 201] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 35, 36, 37] set([0, 1, 2, 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]) total number of confs: 526 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242001 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242001 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242001/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242001 Building REAL300025242002 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242002' /scratch/stefan/7787021/working/building/REAL300025242002 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242002 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242002/0 /scratch/stefan/7787021/working/building/REAL300025242002 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/891 `/scratch/stefan/7787021/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)COCC1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242002.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242002 none CC(CCNC(=O)COCC1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 30, 32, 32, 33, 33, 33, 33, 102, 132, 141, 201, 201, 201, 201, 21, 30, 14, 21, 11, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 33, 33, 33, 102, 102, 141, 141, 201, 201, 201, 201, 201, 201, 201, 201, 201, 30, 30, 30, 14, 14, 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: 672 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: REAL300025242002 none CC(CCNC(=O)COCC1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 74, 74, 46, 46, 21, 46, 9, 5, 1, 1, 1, 1, 1, 1, 75, 91, 91, 96, 96, 126, 153, 201, 201, 201, 201, 201, 75, 75, 75, 75, 74, 74, 74, 74, 46, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 126, 126, 201] 201 rigid atoms, others: [45, 43, 40, 9, 10, 11, 12, 13, 14, 44, 48, 46, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 706 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242002 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242002 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242002/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242002 Building REAL300025242003 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242003' /scratch/stefan/7787021/working/building/REAL300025242003 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242003 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242003/0 /scratch/stefan/7787021/working/building/REAL300025242003 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/892 `/scratch/stefan/7787021/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCCC1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242003.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242003 none CC(CCNC(=O)CCCC1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 30, 30, 30, 30, 113, 132, 141, 201, 201, 201, 201, 30, 30, 23, 29, 12, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 113, 113, 141, 141, 141, 141, 201, 201, 201, 201, 201, 201, 201, 201, 201, 30, 30, 30, 23, 23, 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: 853 number of broken/clashed sets: 163 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242003 none CC(CCNC(=O)CCCC1CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 7, 23, 3, 3, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 62, 98, 201, 201, 201, 201, 201, 23, 23, 23, 23, 23, 23, 23, 23, 23, 7, 7, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 62, 62, 201] 201 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56]) total number of confs: 506 number of broken/clashed sets: 163 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242003 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242003 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242003/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242003 Building REAL300025242004 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242004' /scratch/stefan/7787021/working/building/REAL300025242004 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242004 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242004/0 /scratch/stefan/7787021/working/building/REAL300025242004 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/893 `/scratch/stefan/7787021/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CN(C)C(=O)N1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242004.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242004 none CC(CCNC(=O)C1=CN(C)C(=O)N1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 89, 108, 128, 140, 144, 144, 144, 201, 201, 201, 201, 201, 201, 201, 72, 89, 29, 72, 13, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 128, 128, 140, 140, 144, 201, 201, 201, 201, 201, 201, 201, 89, 89, 89, 29, 29, 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: 694 number of broken/clashed sets: 130 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242004 none CC(CCNC(=O)C1=CN(C)C(=O)N1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 18, 17, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 28, 34, 34, 39, 39, 71, 114, 201, 201, 201, 201, 201, 28, 28, 28, 28, 21, 21, 17, 17, 9, 1, 2, 2, 2, 2, 2, 2, 34, 34, 34, 71, 71, 201] 201 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 560 number of broken/clashed sets: 130 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242004 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242004 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242004/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242004 Building REAL300025242005 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242005' /scratch/stefan/7787021/working/building/REAL300025242005 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242005 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242005/0 /scratch/stefan/7787021/working/building/REAL300025242005 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/894 `/scratch/stefan/7787021/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NSC(C)=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242005.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242005 none CC1=NSC(C)=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need 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, 80, 80, 80, 78, 72, 68, 63, 68, 52, 63, 22, 52, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 80, 78, 78, 72, 72, 68, 68, 68, 68, 63, 63, 63, 22, 22, 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: 479 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: REAL300025242005 none CC1=NSC(C)=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations 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, 6, 12, 16, 22, 22, 24, 24, 32, 32, 63, 102, 201, 201, 201, 201, 201, 2, 2, 2, 2, 2, 2, 7, 12, 12, 16, 16, 22, 22, 22, 22, 24, 24, 24, 63, 63, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 537 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242005 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242005 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242005/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242005 Building REAL300025242006 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242006' /scratch/stefan/7787021/working/building/REAL300025242006 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242006 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242006/0 /scratch/stefan/7787021/working/building/REAL300025242006 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/895 `/scratch/stefan/7787021/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CC(C)CC(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242006.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242006 none CC(CCNC(=O)C1CC(C)CC(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 77, 83, 84, 88, 88, 88, 88, 201, 201, 201, 201, 201, 201, 201, 59, 77, 24, 58, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 84, 84, 88, 88, 88, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 77, 77, 77, 24, 24, 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: 659 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: REAL300025242006 none CC(CCNC(=O)C1CC(C)CC(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 16, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 24, 28, 28, 33, 33, 66, 109, 201, 201, 201, 201, 201, 24, 24, 24, 24, 19, 19, 16, 16, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 28, 28, 28, 66, 66, 201] 201 rigid atoms, others: [45, 43, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 44, 40, 50, 41, 39, 49, 42, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47, 48, 51, 52, 53, 54, 55, 56]) total number of confs: 521 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242006 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242006 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242006/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242006 Building REAL300025242007 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242007' /scratch/stefan/7787021/working/building/REAL300025242007 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242007 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242007/0 /scratch/stefan/7787021/working/building/REAL300025242007 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/896 `/scratch/stefan/7787021/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@H]1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242007.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242007 none CC(=O)N1CCC[C@@H]1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 168, 201, 168, 168, 168, 168, 132, 168, 132, 132, 125, 109, 99, 85, 99, 62, 85, 26, 62, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 168, 168, 168, 168, 168, 168, 132, 125, 125, 109, 109, 99, 99, 99, 99, 85, 85, 85, 26, 26, 1] 201 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: 799 number of broken/clashed sets: 97 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242007 none CC(=O)N1CCC[C@@H]1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 14, 18, 18, 21, 21, 25, 25, 47, 77, 168, 168, 168, 168, 168, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 12, 12, 15, 15, 18, 18, 18, 18, 21, 21, 21, 47, 47, 168] 201 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 35, 36, 33, 31] set([0, 2, 10, 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, 49, 50, 51]) total number of confs: 417 number of broken/clashed sets: 97 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242007 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242007 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242007/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242007 Building REAL300025242008 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242008' /scratch/stefan/7787021/working/building/REAL300025242008 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242008 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242008/0 /scratch/stefan/7787021/working/building/REAL300025242008 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/897 `/scratch/stefan/7787021/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCCC(C)(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242008.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242008 none CC(CCNC(=O)C1CCCC(C)(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 76, 82, 83, 87, 87, 87, 87, 201, 201, 201, 201, 201, 201, 201, 59, 76, 25, 59, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 83, 83, 87, 87, 87, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 76, 76, 76, 25, 25, 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: 660 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: REAL300025242008 none CC(CCNC(=O)C1CCCC(C)(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 16, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 24, 28, 28, 33, 33, 66, 108, 201, 201, 201, 201, 201, 24, 24, 24, 24, 19, 19, 16, 16, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 28, 28, 28, 66, 66, 201] 201 rigid atoms, others: [45, 11, 36, 5, 38, 7, 8, 9, 10, 39, 12, 13, 14, 44, 40, 50, 43, 41, 49, 42, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47, 48, 51, 52, 53, 54, 55, 56]) total number of confs: 521 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242008 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242008 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242008/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242008 Building REAL300025242009 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242009' /scratch/stefan/7787021/working/building/REAL300025242009 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242009 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242009/0 /scratch/stefan/7787021/working/building/REAL300025242009 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/898 `/scratch/stefan/7787021/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCC(C)(C)CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242009.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242009 none CC(CCNC(=O)C1CCC(C)(C)CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 80, 86, 90, 94, 94, 94, 94, 201, 201, 201, 201, 201, 201, 201, 64, 80, 27, 63, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 90, 90, 94, 94, 94, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 80, 80, 80, 27, 27, 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: 674 number of broken/clashed sets: 93 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242009 none CC(CCNC(=O)C1CCC(C)(C)CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 23, 26, 26, 31, 31, 64, 107, 201, 201, 201, 201, 201, 23, 23, 23, 23, 18, 18, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 26, 26, 26, 64, 64, 201] 201 rigid atoms, others: [11, 36, 5, 38, 7, 8, 9, 10, 39, 12, 13, 14, 47, 48, 40, 50, 43, 41, 49, 42, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46, 51, 52, 53, 54, 55, 56]) total number of confs: 527 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242009 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242009 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242009/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242009 Building REAL300025242010 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242010' /scratch/stefan/7787021/working/building/REAL300025242010 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242010 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242010/0 /scratch/stefan/7787021/working/building/REAL300025242010 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/899 `/scratch/stefan/7787021/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC=C(CF)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242010.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242010 none CC(CCNC(=O)C1=CC=C(CF)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [131, 124, 131, 151, 168, 170, 170, 170, 201, 201, 170, 201, 201, 201, 201, 86, 124, 32, 85, 13, 1, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 151, 151, 168, 168, 170, 201, 201, 201, 201, 201, 201, 124, 124, 124, 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: 870 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: REAL300025242010 none CC(CCNC(=O)C1=CC=C(CF)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [12, 8, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 1, 1, 12, 13, 13, 18, 18, 47, 76, 201, 201, 201, 201, 201, 12, 12, 12, 12, 9, 9, 7, 7, 3, 1, 1, 6, 6, 1, 1, 13, 13, 13, 47, 47, 201] 201 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 13, 14, 40, 41, 37] set([0, 1, 2, 3, 4, 6, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 42, 43, 44, 45, 46, 47]) total number of confs: 456 number of broken/clashed sets: 126 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242010 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242010 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242010/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242010 Building REAL300025242011 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242011' /scratch/stefan/7787021/working/building/REAL300025242011 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242011 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242011/0 /scratch/stefan/7787021/working/building/REAL300025242011 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/900 `/scratch/stefan/7787021/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(CC(C)C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242011.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242011 none CCCC(CC(C)C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 101, 164, 164, 164, 164, 101, 101, 91, 83, 73, 66, 73, 52, 66, 25, 51, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 164, 164, 164, 164, 164, 164, 164, 164, 164, 164, 101, 91, 91, 83, 83, 73, 73, 73, 73, 66, 66, 66, 25, 25, 1] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26, 58] 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, 56, 57]) total number of confs: 974 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242011 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242011 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242011/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242011 Building REAL300025242012 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242012' /scratch/stefan/7787021/working/building/REAL300025242012 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242012 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242012/0 /scratch/stefan/7787021/working/building/REAL300025242012 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/901 `/scratch/stefan/7787021/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCCCC1(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242012.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242012 none CC(CCNC(=O)C1CCCCC1(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 102, 123, 145, 158, 163, 163, 163, 201, 201, 201, 201, 201, 201, 201, 65, 102, 28, 64, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 145, 145, 158, 158, 163, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 102, 102, 102, 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: 805 number of broken/clashed sets: 66 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242012 none CC(CCNC(=O)C1CCCCC1(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 11, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 18, 25, 25, 37, 37, 65, 104, 201, 201, 201, 201, 201, 18, 18, 18, 18, 12, 12, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 25, 25, 25, 65, 65, 201] 201 rigid atoms, others: [11, 36, 5, 38, 7, 8, 9, 10, 39, 12, 13, 14, 44, 40, 43, 41, 42, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 528 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242012 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242012 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242012/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242012 Building REAL300025242013 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242013' /scratch/stefan/7787021/working/building/REAL300025242013 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242013 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242013/0 /scratch/stefan/7787021/working/building/REAL300025242013 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/902 `/scratch/stefan/7787021/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1(C)CCC(C)CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242013.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242013 none CC(CCNC(=O)C1(C)CCC(C)CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 73, 85, 97, 102, 115, 115, 115, 201, 201, 201, 201, 201, 201, 201, 52, 73, 24, 51, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 97, 97, 102, 102, 115, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 73, 73, 73, 24, 24, 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: 785 number of broken/clashed sets: 83 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242013 none CC(CCNC(=O)C1(C)CCC(C)CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 19, 25, 25, 34, 34, 63, 102, 201, 201, 201, 201, 201, 19, 19, 19, 19, 13, 13, 11, 11, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 25, 25, 25, 63, 63, 201] 201 rigid atoms, others: [11, 5, 7, 8, 9, 10, 39, 12, 13, 14, 47, 48, 40, 50, 43, 41, 49, 42] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 51, 52, 53, 54, 55, 56]) total number of confs: 515 number of broken/clashed sets: 83 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242013 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242013 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242013/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242013 Building REAL300025242014 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242014' /scratch/stefan/7787021/working/building/REAL300025242014 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242014 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242014/0 /scratch/stefan/7787021/working/building/REAL300025242014 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/903 `/scratch/stefan/7787021/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)[C@H]1[C@H]2[C@@H]1[C@@H]1CC[C@H]2C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242014.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242014 none CC(CCNC(=O)[C@H]1[C@H]2[C@@H]1[C@@H]1CC[C@H]2C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 7, 5, 7, 5, 7, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [70, 64, 70, 80, 85, 85, 85, 85, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 50, 64, 25, 49, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 80, 80, 85, 85, 85, 201, 201, 201, 201, 201, 201, 64, 64, 64, 25, 25, 1] 201 rigid atoms, others: [52, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 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, 47, 48, 49, 50, 51]) total number of confs: 705 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: REAL300025242014 none CC(CCNC(=O)[C@H]1[C@H]2[C@@H]1[C@@H]1CC[C@H]2C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 7, 5, 7, 5, 7, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [24, 18, 15, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 26, 26, 32, 32, 64, 103, 201, 201, 201, 201, 201, 24, 24, 24, 24, 19, 19, 15, 15, 11, 1, 1, 1, 1, 1, 1, 26, 26, 26, 64, 64, 201] 201 rigid atoms, others: [18, 43, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 44, 19, 46, 41, 45, 42] set([0, 1, 2, 3, 4, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49, 50, 51, 52]) total number of confs: 516 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242014 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242014 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242014/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242014 Building REAL300025242015 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242015' /scratch/stefan/7787021/working/building/REAL300025242015 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242015 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242015/0 /scratch/stefan/7787021/working/building/REAL300025242015 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/904 `/scratch/stefan/7787021/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1CCCO1)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242015.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242015 none CC(CC1CCCO1)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 106, 194, 201, 201, 201, 201, 201, 106, 106, 88, 84, 56, 56, 56, 42, 56, 29, 42, 13, 1, 1, 1, 1, 1, 1, 1, 194, 194, 194, 194, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 88, 88, 84, 84, 56, 56, 56, 56, 56, 56, 56, 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: 912 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242015 none CC(CC1CCCO1)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 15, 17, 20, 20, 20, 20, 46, 46, 65, 101, 201, 201, 201, 201, 201, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 15, 15, 17, 17, 20, 20, 20, 20, 20, 20, 20, 65, 65, 201] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 39, 34, 35, 36, 38, 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, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 525 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242015 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242015 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242015/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242015 Building REAL300025242016 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242016' /scratch/stefan/7787021/working/building/REAL300025242016 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242016 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242016/0 /scratch/stefan/7787021/working/building/REAL300025242016 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/905 `/scratch/stefan/7787021/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=CO1) `REAL300025242016.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242016 none CC(C)C1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=CO1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 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, 201, 201, 129, 129, 129, 128, 123, 117, 103, 117, 72, 103, 31, 72, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 128, 128, 123, 123, 117, 117, 117, 117, 103, 103, 103, 31, 31, 1, 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]) total number of confs: 621 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242016 none CC(C)C1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=CO1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 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: [2, 1, 2, 1, 1, 1, 8, 8, 8, 14, 15, 21, 21, 26, 26, 31, 31, 57, 95, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 14, 14, 16, 16, 21, 21, 21, 21, 26, 26, 26, 57, 57, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 49, 50, 24, 25, 26] set([0, 2, 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: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242016 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242016 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242016/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242016 Building REAL300025242017 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242017' /scratch/stefan/7787021/working/building/REAL300025242017 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242017 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242017/0 /scratch/stefan/7787021/working/building/REAL300025242017 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/906 `/scratch/stefan/7787021/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CC(C(C)(C)C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242017.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242017 none CC(CCNC(=O)C1CC(C(C)(C)C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 79, 84, 84, 84, 84, 84, 84, 201, 201, 201, 201, 201, 201, 201, 64, 79, 30, 64, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 84, 84, 84, 84, 84, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 79, 79, 30, 30, 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: 614 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: REAL300025242017 none CC(CCNC(=O)C1CC(C(C)(C)C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 8, 8, 1, 8, 1, 1, 1, 1, 2, 2, 2, 1, 15, 19, 19, 25, 25, 56, 93, 201, 201, 201, 201, 201, 15, 15, 15, 15, 15, 15, 15, 15, 8, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 19, 19, 19, 56, 56, 201] 201 rigid atoms, others: [36, 5, 38, 7, 8, 9, 10, 39, 14, 49, 50, 37] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 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, 51, 52, 53, 54, 55, 56]) total number of confs: 490 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242017 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242017 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242017/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242017 Building REAL300025242018 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242018' /scratch/stefan/7787021/working/building/REAL300025242018 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242018 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242018/0 /scratch/stefan/7787021/working/building/REAL300025242018 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/907 `/scratch/stefan/7787021/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCC(C)C(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242018.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242018 none CC(CCNC(=O)C1CCC(C)C(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 81, 87, 90, 94, 94, 94, 94, 201, 201, 201, 201, 201, 201, 201, 63, 81, 26, 63, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 90, 90, 94, 94, 94, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 81, 81, 81, 26, 26, 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: 668 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242018 none CC(CCNC(=O)C1CCC(C)C(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 16, 13, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 23, 27, 27, 32, 32, 65, 108, 201, 201, 201, 201, 201, 23, 23, 23, 23, 16, 16, 13, 13, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 65, 65, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 51, 52, 53, 54, 55, 56]) total number of confs: 528 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242018 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242018 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242018/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242018 Building REAL300025242019 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242019' /scratch/stefan/7787021/working/building/REAL300025242019 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242019 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242019/0 /scratch/stefan/7787021/working/building/REAL300025242019 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/908 `/scratch/stefan/7787021/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CCCCC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242019.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242019 none COC1CCCCC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 201, 201, 171, 157, 133, 105, 133, 73, 105, 30, 73, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 171, 171, 157, 157, 133, 133, 133, 133, 105, 105, 105, 30, 30, 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: 796 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: REAL300025242019 none COC1CCCCC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 8, 10, 15, 15, 27, 27, 35, 35, 65, 94, 201, 201, 201, 201, 201, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 11, 11, 15, 15, 15, 15, 27, 27, 27, 65, 65, 201] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 39, 34, 35, 36, 33, 38, 37, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 505 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242019 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242019 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242019/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242019 Building REAL300025242020 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242020' /scratch/stefan/7787021/working/building/REAL300025242020 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242020 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242020/0 /scratch/stefan/7787021/working/building/REAL300025242020 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/909 `/scratch/stefan/7787021/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCOCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242020.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242020 none C=CCCOCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens need 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, 163, 132, 51, 51, 51, 44, 44, 40, 31, 40, 31, 31, 29, 31, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 170, 170, 132, 132, 51, 44, 44, 44, 44, 40, 40, 40, 40, 31, 31, 31, 29, 29, 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: 810 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242020 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242020 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242020/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242020 Building REAL300025242021 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242021' /scratch/stefan/7787021/working/building/REAL300025242021 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242021 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242021/0 /scratch/stefan/7787021/working/building/REAL300025242021 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/910 `/scratch/stefan/7787021/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242021.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242021 none C=CCOC(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 156, 107, 156, 107, 107, 76, 76, 58, 38, 58, 38, 38, 34, 38, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 156, 156, 156, 156, 107, 76, 76, 76, 76, 58, 58, 58, 58, 38, 38, 38, 34, 34, 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: 897 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242021 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242021 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242021/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242021 Building REAL300025242022 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242022' /scratch/stefan/7787021/working/building/REAL300025242022 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242022 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242022/0 /scratch/stefan/7787021/working/building/REAL300025242022 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/911 `/scratch/stefan/7787021/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)S1) `REAL300025242022.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242022 none CCC1=NC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 111, 111, 111, 111, 110, 110, 110, 90, 87, 61, 53, 61, 40, 53, 28, 40, 13, 1, 1, 1, 1, 1, 1, 1, 111, 201, 201, 201, 201, 201, 111, 110, 90, 90, 87, 87, 61, 61, 61, 61, 53, 53, 53, 28, 28, 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: 1015 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: REAL300025242022 none CCC1=NC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 3, 3, 3, 8, 8, 12, 12, 15, 15, 25, 25, 31, 48, 111, 111, 111, 111, 111, 1, 6, 6, 6, 5, 5, 1, 3, 8, 8, 8, 8, 12, 12, 12, 12, 15, 15, 15, 31, 31, 111] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 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: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242022 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242022 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242022/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242022 Building REAL300025242023 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242023' /scratch/stefan/7787021/working/building/REAL300025242023 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242023 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242023/0 /scratch/stefan/7787021/working/building/REAL300025242023 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/912 `/scratch/stefan/7787021/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242023.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242023 none CC1=CN=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 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, 7] 0 hydrogens need 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, 139, 201, 201, 102, 102, 102, 101, 96, 93, 83, 93, 64, 83, 29, 64, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 102, 101, 101, 96, 96, 93, 93, 93, 93, 83, 83, 83, 29, 29, 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: 714 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242023 none CC1=CN=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations 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, 17, 18, 24, 24, 27, 27, 31, 31, 67, 102, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 10, 17, 17, 19, 19, 24, 24, 24, 24, 27, 27, 27, 67, 67, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 529 number of broken/clashed sets: 113 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242023 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242023 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242023/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242023 Building REAL300025242024 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242024' /scratch/stefan/7787021/working/building/REAL300025242024 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242024 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242024/0 /scratch/stefan/7787021/working/building/REAL300025242024 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/913 `/scratch/stefan/7787021/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCC1(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242024.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242024 none CC(CCNC(=O)C1CCC1(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [110, 96, 110, 123, 134, 134, 134, 134, 201, 201, 201, 201, 201, 69, 96, 28, 68, 12, 1, 1, 1, 1, 1, 1, 1, 110, 110, 110, 110, 123, 123, 134, 134, 134, 201, 201, 201, 201, 201, 96, 96, 96, 28, 28, 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: 736 number of broken/clashed sets: 104 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242024 none CC(CCNC(=O)C1CCC1(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [21, 15, 11, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 26, 26, 34, 34, 72, 115, 201, 201, 201, 201, 201, 21, 21, 21, 21, 15, 15, 11, 11, 8, 1, 1, 1, 1, 1, 26, 26, 26, 72, 72, 201] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44]) total number of confs: 549 number of broken/clashed sets: 104 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242024 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242024 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242024/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242024 Building REAL300025242025 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242025' /scratch/stefan/7787021/working/building/REAL300025242025 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242025 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242025/0 /scratch/stefan/7787021/working/building/REAL300025242025 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/914 `/scratch/stefan/7787021/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=NSC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242025.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242025 none CC(CCNC(=O)C1=NSC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 1, 8, 14, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 101, 117, 150, 171, 201, 201, 201, 201, 201, 201, 201, 60, 101, 27, 59, 13, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 150, 150, 171, 171, 201, 201, 201, 101, 101, 101, 27, 27, 1] 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]) total number of confs: 836 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242025 none CC(CCNC(=O)C1=NSC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 1, 8, 14, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 15, 25, 25, 39, 39, 68, 107, 201, 201, 201, 201, 201, 15, 15, 15, 15, 8, 8, 7, 7, 2, 1, 1, 25, 25, 25, 68, 68, 201] 201 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 508 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242025 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242025 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242025/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242025 Building REAL300025242026 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242026' /scratch/stefan/7787021/working/building/REAL300025242026 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242026 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242026/0 /scratch/stefan/7787021/working/building/REAL300025242026 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/915 `/scratch/stefan/7787021/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=NNC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1) `REAL300025242026.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242026 none CCOC1=NNC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 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, 7, 7, 7] 0 hydrogens need 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, 199, 199, 199, 199, 199, 199, 199, 133, 131, 104, 75, 104, 59, 76, 38, 59, 13, 1, 1, 1, 1, 1, 1, 1, 199, 201, 201, 201, 201, 201, 199, 199, 133, 133, 131, 131, 104, 104, 104, 104, 76, 76, 76, 38, 38, 1, 199] 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]) total number of confs: 835 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: REAL300025242026 none CCOC1=NNC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 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, 7, 7, 7] 0 hydrogens 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, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 11, 17, 17, 21, 21, 42, 42, 62, 99, 199, 199, 199, 199, 199, 1, 6, 6, 6, 5, 5, 1, 4, 10, 10, 11, 11, 17, 17, 17, 17, 21, 21, 21, 62, 62, 199, 1] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 48, 26] set([0, 1, 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: 521 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242026 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242026 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242026/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242026 Building REAL300025242027 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242027' /scratch/stefan/7787021/working/building/REAL300025242027 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242027 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242027/0 /scratch/stefan/7787021/working/building/REAL300025242027 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/916 `/scratch/stefan/7787021/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C(C)S1) `REAL300025242027.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242027 none CC1=NC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 200, 200, 200, 176, 150, 111, 94, 111, 60, 94, 28, 60, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 200, 176, 176, 150, 150, 111, 111, 111, 111, 94, 94, 94, 28, 28, 1, 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]) total number of confs: 861 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: REAL300025242027 none CC1=NC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 11, 13, 22, 22, 33, 33, 40, 40, 67, 106, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 4, 10, 10, 14, 14, 22, 22, 22, 22, 33, 33, 33, 67, 67, 201, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25] set([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: 530 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242027 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242027 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242027/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242027 Building REAL300025242028 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242028' /scratch/stefan/7787021/working/building/REAL300025242028 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242028 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242028/0 /scratch/stefan/7787021/working/building/REAL300025242028 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/917 `/scratch/stefan/7787021/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C(C)C1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242028.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242028 none CC(CCNC(=O)C(C)C1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 93, 94, 107, 118, 123, 123, 123, 201, 201, 201, 201, 201, 82, 93, 31, 82, 13, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 107, 107, 118, 118, 123, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 93, 93, 93, 31, 31, 1] 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]) total number of confs: 824 number of broken/clashed sets: 105 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242028 none CC(CCNC(=O)C(C)C1CCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 23, 21, 11, 11, 3, 11, 1, 3, 1, 1, 1, 1, 31, 31, 31, 37, 37, 75, 112, 201, 201, 201, 201, 201, 31, 31, 31, 31, 25, 25, 21, 21, 11, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 75, 75, 201] 201 rigid atoms, others: [43, 38, 7, 40, 9, 10, 11, 12, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 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, 45, 46, 47, 48, 49, 50]) total number of confs: 541 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242028 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242028 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242028/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242028 Building REAL300025242029 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242029' /scratch/stefan/7787021/working/building/REAL300025242029 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242029 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242029/0 /scratch/stefan/7787021/working/building/REAL300025242029 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/918 `/scratch/stefan/7787021/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1C=CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242029.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242029 none CC(CCNC(=O)CC1C=CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 63, 67, 68, 68, 68, 194, 201, 201, 201, 201, 201, 53, 60, 26, 53, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 63, 63, 67, 67, 68, 194, 194, 201, 201, 201, 201, 201, 201, 201, 201, 201, 60, 60, 60, 26, 26, 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: 784 number of broken/clashed sets: 116 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242029 none CC(CCNC(=O)CC1C=CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 24, 22, 18, 18, 4, 18, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 29, 29, 65, 101, 201, 201, 201, 201, 201, 25, 25, 25, 25, 24, 24, 22, 22, 18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 65, 65, 201] 201 rigid atoms, others: [45, 43, 37, 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, 46, 47, 48, 49, 50, 51]) total number of confs: 507 number of broken/clashed sets: 116 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242029 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242029 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242029/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242029 Building REAL300025242030 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242030' /scratch/stefan/7787021/working/building/REAL300025242030 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242030 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242030/0 /scratch/stefan/7787021/working/building/REAL300025242030 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/919 `/scratch/stefan/7787021/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1=CC=C(F)C=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242030.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242030 none CC(CCNC(=O)CC1=CC=C(F)C=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 1, 1, 1, 1, 15, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 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, 44, 54, 65, 66, 66, 66, 201, 201, 201, 201, 201, 201, 201, 35, 44, 17, 35, 11, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 54, 54, 65, 65, 66, 201, 201, 201, 201, 201, 44, 44, 44, 17, 17, 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: 808 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242030 none CC(CCNC(=O)CC1=CC=C(F)C=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 1, 1, 1, 1, 15, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 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: [26, 22, 14, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 37, 37, 73, 112, 201, 201, 201, 201, 201, 26, 26, 26, 26, 22, 22, 14, 14, 9, 3, 3, 1, 1, 1, 26, 26, 26, 73, 73, 201] 201 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 14, 40, 39] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46]) total number of confs: 561 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242030 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242030 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242030/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242030 Building REAL300025242031 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242031' /scratch/stefan/7787021/working/building/REAL300025242031 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242031 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242031/0 /scratch/stefan/7787021/working/building/REAL300025242031 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/920 `/scratch/stefan/7787021/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CC1) `REAL300025242031.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242031 none CCOCC1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 172, 79, 79, 79, 74, 74, 47, 47, 47, 36, 47, 25, 36, 12, 1, 1, 1, 1, 1, 1, 1, 172, 172, 201, 201, 201, 201, 201, 201, 201, 79, 74, 74, 74, 74, 47, 47, 47, 47, 47, 47, 47, 25, 25, 1, 172, 172, 172, 172] 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: 769 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: REAL300025242031 none CCOCC1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 1, 1, 6, 6, 6, 7, 7, 9, 9, 9, 9, 23, 23, 37, 68, 172, 172, 172, 172, 172, 1, 1, 13, 13, 13, 13, 13, 6, 6, 6, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 37, 37, 172, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 48, 49, 50, 51, 24, 25] set([0, 1, 2, 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: 412 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242031 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242031 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242031/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242031 Building REAL300025242032 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242032' /scratch/stefan/7787021/working/building/REAL300025242032 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242032 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242032/0 /scratch/stefan/7787021/working/building/REAL300025242032 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/921 `/scratch/stefan/7787021/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1CC(F)(F)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242032.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242032 none CC(CCNC(=O)CC1CC(F)(F)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [65, 65, 65, 65, 69, 69, 69, 69, 171, 201, 201, 201, 201, 201, 57, 65, 28, 57, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 65, 69, 69, 69, 171, 171, 201, 201, 201, 201, 201, 65, 65, 65, 28, 28, 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: 773 number of broken/clashed sets: 148 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242032 none CC(CCNC(=O)CC1CC(F)(F)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [26, 26, 25, 23, 23, 5, 23, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 27, 27, 62, 99, 201, 201, 201, 201, 201, 26, 26, 26, 26, 26, 26, 25, 25, 23, 5, 5, 1, 1, 1, 1, 1, 26, 26, 26, 62, 62, 201] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 40, 41] 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, 42, 43, 44, 45, 46, 47]) total number of confs: 488 number of broken/clashed sets: 148 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242032 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242032 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242032/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242032 Building REAL300025242033 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242033' /scratch/stefan/7787021/working/building/REAL300025242033 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242033 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242033/0 /scratch/stefan/7787021/working/building/REAL300025242033 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/922 `/scratch/stefan/7787021/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CC2C=CC1O2)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242033.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242033 none CC(CCNC(=O)C1CC2C=CC1O2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 100, 115, 152, 175, 196, 196, 196, 201, 201, 201, 201, 201, 201, 61, 100, 28, 61, 13, 1, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 152, 152, 175, 175, 196, 201, 201, 201, 201, 201, 201, 201, 100, 100, 100, 28, 28, 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: 850 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: REAL300025242033 none CC(CCNC(=O)C1CC2C=CC1O2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 20, 28, 28, 37, 37, 67, 106, 201, 201, 201, 201, 201, 20, 20, 20, 20, 13, 13, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 67, 67, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47]) total number of confs: 511 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242033 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242033 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242033/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242033 Building REAL300025242034 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242034' /scratch/stefan/7787021/working/building/REAL300025242034 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242034 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242034/0 /scratch/stefan/7787021/working/building/REAL300025242034 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/923 `/scratch/stefan/7787021/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(C)(F)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242034.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242034 none CCCCC(C)(F)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 189, 131, 189, 189, 131, 131, 101, 101, 83, 59, 83, 46, 60, 31, 46, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 189, 189, 189, 131, 101, 101, 101, 101, 83, 83, 83, 83, 60, 60, 60, 31, 31, 1] 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]) total number of confs: 904 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242034 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242034 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242034/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242034 Building REAL300025242035 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242035' /scratch/stefan/7787021/working/building/REAL300025242035 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242035 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242035/0 /scratch/stefan/7787021/working/building/REAL300025242035 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/924 `/scratch/stefan/7787021/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CCCC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242035.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242035 none COC1CCCC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 156, 156, 156, 152, 124, 102, 91, 102, 62, 91, 31, 62, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 156, 152, 152, 124, 124, 102, 102, 102, 102, 91, 91, 91, 31, 31, 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: 821 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242035 none COC1CCCC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 14, 19, 24, 24, 26, 26, 29, 29, 61, 97, 201, 201, 201, 201, 201, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 14, 14, 19, 19, 24, 24, 24, 24, 26, 26, 26, 61, 61, 201] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 35, 36, 29, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 519 number of broken/clashed sets: 136 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242035 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242035 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242035/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242035 Building REAL300025242036 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242036' /scratch/stefan/7787021/working/building/REAL300025242036 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242036 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242036/0 /scratch/stefan/7787021/working/building/REAL300025242036 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/925 `/scratch/stefan/7787021/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1COC(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242036.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242036 none CC(CCNC(=O)C1COC(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 85, 94, 102, 109, 109, 109, 109, 201, 201, 201, 201, 201, 70, 85, 28, 69, 13, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 102, 102, 109, 109, 109, 201, 201, 201, 201, 201, 201, 201, 201, 201, 85, 85, 85, 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: 714 number of broken/clashed sets: 98 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242036 none CC(CCNC(=O)C1COC(C)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 15, 14, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 25, 25, 31, 31, 69, 109, 201, 201, 201, 201, 201, 21, 21, 21, 21, 16, 16, 14, 14, 9, 1, 1, 1, 1, 2, 2, 2, 1, 1, 25, 25, 25, 69, 69, 201] 201 rigid atoms, others: [34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 41, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 43, 44, 45, 46, 47, 48]) total number of confs: 531 number of broken/clashed sets: 98 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242036 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242036 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242036/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242036 Building REAL300025242037 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242037' /scratch/stefan/7787021/working/building/REAL300025242037 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242037 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242037/0 /scratch/stefan/7787021/working/building/REAL300025242037 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/926 `/scratch/stefan/7787021/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCCC2CC21)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242037.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242037 none CC(CCNC(=O)C1CCCC2CC21)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 104, 118, 123, 130, 130, 130, 130, 201, 201, 201, 201, 201, 201, 77, 104, 29, 77, 13, 1, 1, 1, 1, 1, 1, 1, 118, 118, 118, 118, 123, 123, 130, 130, 130, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 104, 104, 104, 29, 29, 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: 701 number of broken/clashed sets: 107 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242037 none CC(CCNC(=O)C1CCCC2CC21)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 16, 15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 23, 27, 27, 32, 32, 72, 120, 201, 201, 201, 201, 201, 23, 23, 23, 23, 17, 17, 15, 15, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 72, 72, 201] 201 rigid atoms, others: [45, 35, 36, 5, 38, 7, 8, 9, 10, 39, 12, 13, 44, 11, 40, 43, 41, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 46, 47, 48, 49, 50, 51]) total number of confs: 531 number of broken/clashed sets: 107 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242037 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242037 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242037/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242037 Building REAL300025242038 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242038' /scratch/stefan/7787021/working/building/REAL300025242038 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242038 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242038/0 /scratch/stefan/7787021/working/building/REAL300025242038 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/927 `/scratch/stefan/7787021/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1CCC2CC21)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242038.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242038 none CC(CCNC(=O)CC1CCC2CC21)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 77, 83, 83, 83, 83, 180, 201, 201, 201, 201, 201, 63, 70, 28, 63, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 77, 77, 83, 83, 83, 180, 180, 201, 201, 201, 201, 201, 201, 201, 201, 201, 70, 70, 70, 28, 28, 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: 776 number of broken/clashed sets: 140 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242038 none CC(CCNC(=O)CC1CCC2CC21)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 29, 25, 22, 22, 5, 22, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 33, 33, 68, 105, 201, 201, 201, 201, 201, 32, 32, 32, 32, 29, 29, 25, 25, 22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 68, 68, 201] 201 rigid atoms, others: [45, 11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 44, 40, 43, 41, 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, 46, 47, 48, 49, 50, 51]) total number of confs: 526 number of broken/clashed sets: 140 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242038 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242038 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242038/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242038 Building REAL300025242039 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242039' /scratch/stefan/7787021/working/building/REAL300025242039 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242039 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242039/0 /scratch/stefan/7787021/working/building/REAL300025242039 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/928 `/scratch/stefan/7787021/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCC2CC2C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242039.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242039 none CC(CCNC(=O)C1CCC2CC2C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 89, 95, 98, 102, 102, 102, 102, 201, 201, 201, 201, 201, 201, 70, 89, 30, 69, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 98, 98, 102, 102, 102, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 89, 89, 89, 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: 692 number of broken/clashed sets: 89 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242039 none CC(CCNC(=O)C1CCC2CC2C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 14, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 23, 27, 27, 33, 33, 67, 111, 201, 201, 201, 201, 201, 23, 23, 23, 23, 17, 17, 14, 14, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 67, 67, 201] 201 rigid atoms, others: [45, 35, 36, 5, 38, 7, 8, 9, 10, 39, 12, 13, 44, 11, 40, 43, 41, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 46, 47, 48, 49, 50, 51]) total number of confs: 528 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242039 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242039 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242039/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242039 Building REAL300025242040 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242040' /scratch/stefan/7787021/working/building/REAL300025242040 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242040 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242040/0 /scratch/stefan/7787021/working/building/REAL300025242040 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/929 `/scratch/stefan/7787021/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(OC)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242040.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242040 none CCC(C)C(OC)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 201, 137, 175, 175, 137, 137, 127, 110, 91, 76, 91, 51, 76, 23, 50, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 175, 175, 175, 175, 137, 127, 127, 110, 110, 91, 91, 91, 91, 76, 76, 76, 23, 23, 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: 951 number of broken/clashed sets: 119 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242040 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242040 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242040/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242040 Building REAL300025242041 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242041' /scratch/stefan/7787021/working/building/REAL300025242041 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242041 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242041/0 /scratch/stefan/7787021/working/building/REAL300025242041 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/930 `/scratch/stefan/7787021/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CCC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025242041.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242041 none COC1CCC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 101, 101, 101, 85, 84, 58, 52, 58, 41, 53, 26, 41, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 85, 85, 84, 84, 58, 58, 58, 58, 53, 53, 53, 26, 26, 1, 201, 201] 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]) total number of confs: 735 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242041 none COC1CCC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 19, 19, 20, 20, 42, 42, 60, 95, 201, 201, 201, 201, 201, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 9, 14, 14, 14, 14, 19, 19, 19, 19, 20, 20, 20, 60, 60, 201, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 34, 50, 51, 25, 29, 30, 31] set([0, 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: 492 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242041 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242041 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242041/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242041 Building REAL300025242042 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242042' /scratch/stefan/7787021/working/building/REAL300025242042 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242042 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242042/0 /scratch/stefan/7787021/working/building/REAL300025242042 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/931 `/scratch/stefan/7787021/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CN=C(C2CC2)O1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242042.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242042 none CC(CCNC(=O)C1=CN=C(C2CC2)O1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 29, 25, 13, 13, 13, 13, 12, 12, 13, 1, 1, 1, 1, 13, 36, 36, 36, 40, 40, 79, 112, 201, 201, 201, 201, 201, 36, 36, 36, 36, 29, 29, 25, 25, 13, 13, 1, 1, 1, 1, 1, 36, 36, 36, 79, 79, 201] 201 rigid atoms, others: [37, 38, 39, 40, 41, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47]) total number of confs: 564 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242042 none CC(CCNC(=O)C1=CN=C(C2CC2)O1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [94, 93, 94, 117, 148, 156, 156, 156, 156, 156, 156, 156, 201, 201, 156, 77, 93, 31, 77, 13, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 117, 117, 148, 148, 156, 156, 201, 201, 201, 201, 201, 93, 93, 93, 31, 31, 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: 816 number of broken/clashed sets: 110 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242042 none CC(CCNC(=O)C1=CN=C(C2CC2)O1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 12, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 6, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 13, 13, 1, 9, 10, 10, 12, 12, 27, 45, 156, 156, 156, 156, 156, 9, 9, 9, 9, 6, 6, 5, 5, 2, 1, 13, 13, 13, 13, 13, 10, 10, 10, 27, 27, 156] 201 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 14] set([0, 1, 2, 3, 4, 6, 12, 13, 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, 46, 47]) total number of confs: 319 number of broken/clashed sets: 110 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242042 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242042 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242042/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242042 Building REAL300025242043 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242043' /scratch/stefan/7787021/working/building/REAL300025242043 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242043 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242043/0 /scratch/stefan/7787021/working/building/REAL300025242043 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/932 `/scratch/stefan/7787021/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C[C@@H]1NC(=O)NC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242043.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242043 none CC(CCNC(=O)C[C@@H]1NC(=O)NC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 5, 5, 7, 8, 1, 11, 8, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 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, 91, 93, 98, 125, 129, 129, 129, 183, 201, 201, 201, 201, 201, 201, 201, 76, 91, 31, 76, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 98, 98, 125, 125, 129, 183, 183, 201, 201, 91, 91, 91, 31, 31, 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: 868 number of broken/clashed sets: 111 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242043 none CC(CCNC(=O)C[C@@H]1NC(=O)NC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 5, 5, 7, 8, 1, 11, 8, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 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: [26, 21, 20, 14, 14, 5, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 27, 27, 32, 32, 72, 113, 201, 201, 201, 201, 201, 26, 26, 26, 26, 23, 23, 20, 20, 14, 5, 5, 1, 1, 27, 27, 27, 72, 72, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 40, 39] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 555 number of broken/clashed sets: 111 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242043 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242043 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242043/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242043 Building REAL300025242044 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242044' /scratch/stefan/7787021/working/building/REAL300025242044 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242044 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242044/0 /scratch/stefan/7787021/working/building/REAL300025242044 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/933 `/scratch/stefan/7787021/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CN=C2CCCN12)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242044.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242044 none CC(CCNC(=O)C1=CN=C2CCCN12)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [129, 115, 129, 149, 169, 189, 189, 189, 201, 201, 201, 201, 201, 201, 201, 79, 115, 33, 79, 13, 1, 1, 1, 1, 1, 1, 1, 129, 129, 129, 129, 149, 149, 169, 169, 189, 201, 201, 201, 201, 201, 201, 201, 115, 115, 115, 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: 778 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242044 none CC(CCNC(=O)C1=CN=C2CCCN12)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [18, 14, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 18, 26, 26, 35, 35, 67, 106, 201, 201, 201, 201, 201, 18, 18, 18, 18, 14, 14, 12, 12, 5, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 67, 67, 201] 201 rigid atoms, others: [36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47, 48]) total number of confs: 517 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242044 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242044 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242044/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242044 Building REAL300025242045 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242045' /scratch/stefan/7787021/working/building/REAL300025242045 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300025242045 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242045/0 /scratch/stefan/7787021/working/building/REAL300025242045 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/934 `/scratch/stefan/7787021/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN1CCC[C@H]1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242045.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242045 none C#CCN1CCC[C@H]1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 201, 201, 201, 127, 119, 98, 70, 98, 58, 71, 40, 58, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 127, 127, 119, 119, 98, 98, 98, 98, 71, 71, 71, 40, 40, 1] 201 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: 805 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242045 none C#CCN1CCC[C@H]1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 13, 21, 21, 34, 34, 54, 54, 72, 105, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 10, 10, 14, 14, 21, 21, 21, 21, 34, 34, 34, 72, 72, 201] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36, 31] set([0, 1, 10, 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, 49, 50, 51]) total number of confs: 533 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242045 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025242045/1 /scratch/stefan/7787021/working/building/REAL300025242045 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/935 `/scratch/stefan/7787021/working/3D/935' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC[N@H+]1CCC[C@H]1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242045.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025242045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242045/1/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: REAL300025242045 none C#CC[N@H+]1CCC[C@H]1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.4', 'H', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', '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, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 27, 27, 25, 21, 25, 19, 21, 13, 19, 9, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 27, 27, 27, 27, 25, 25, 25, 25, 21, 21, 21, 13, 13, 1] 49 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: 170 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: REAL300025242045 none C#CC[N@H+]1CCC[C@H]1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.4', 'H', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', '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, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 17, 17, 21, 21, 28, 28, 36, 36, 42, 45, 49, 49, 49, 49, 49, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 17, 17, 17, 17, 21, 21, 21, 21, 28, 28, 28, 42, 42, 49] 49 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 35, 36, 37] set([0, 1, 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: 186 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242045 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `2' /scratch/stefan/7787021/working/building/REAL300025242045/2 /scratch/stefan/7787021/working/building/REAL300025242045 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 2 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/936 `/scratch/stefan/7787021/working/3D/936' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC[N@@H+]1CCC[C@H]1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242045.mol2' -> `2.mol2' `temp.mol2' -> `REAL300025242045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242045/2/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: REAL300025242045 none C#CC[N@@H+]1CCC[C@H]1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.4', 'H', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', '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, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 34, 27, 34, 27, 27, 14, 14, 14, 14, 14, 14, 14, 10, 14, 9, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 27, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 10, 10, 1] 34 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: 98 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: REAL300025242045 none C#CC[N@@H+]1CCC[C@H]1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.4', 'H', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', '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, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 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, 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: [4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 16, 21, 21, 27, 27, 31, 31, 34, 34, 34, 34, 34, 4, 4, 4, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 16, 16, 16, 16, 21, 21, 21, 31, 31, 34] 34 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 35, 36, 37] set([0, 1, 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: 134 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242045 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242045 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242045/0.* 1: /scratch/stefan/7787021/working/building/REAL300025242045/1.* 2: /scratch/stefan/7787021/working/building/REAL300025242045/2.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242045 Building REAL300025242046 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242046' /scratch/stefan/7787021/working/building/REAL300025242046 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242046 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242046/0 /scratch/stefan/7787021/working/building/REAL300025242046 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/937 `/scratch/stefan/7787021/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NC=C1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242046.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242046 none CC1=CC=NC=C1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 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, 7, 7, 7] 0 hydrogens need 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, 54, 54, 54, 54, 54, 40, 39, 40, 29, 40, 22, 29, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 128, 128, 54, 54, 54, 54, 54, 40, 40, 40, 40, 40, 40, 40, 22, 22, 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: 696 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242046 none CC1=CC=NC=C1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 15, 15, 15, 19, 21, 21, 21, 21, 21, 50, 50, 63, 98, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 5, 5, 15, 19, 19, 21, 21, 21, 21, 21, 21, 21, 21, 21, 63, 63, 201] 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, 48, 49]) total number of confs: 498 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242046 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242046 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242046/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242046 Building REAL300025242047 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242047' /scratch/stefan/7787021/working/building/REAL300025242047 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242047 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242047/0 /scratch/stefan/7787021/working/building/REAL300025242047 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/938 `/scratch/stefan/7787021/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)[C@H]1OCCO[C@H]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242047.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242047 none CC(CCNC(=O)[C@H]1OCCO[C@H]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 7, 12, 5, 5, 12, 5, 7, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 101, 121, 148, 166, 177, 177, 177, 201, 201, 201, 201, 201, 201, 201, 201, 68, 101, 30, 68, 13, 1, 1, 1, 1, 1, 1, 1, 121, 121, 121, 121, 148, 148, 166, 166, 177, 201, 201, 201, 201, 201, 201, 201, 101, 101, 101, 30, 30, 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: 836 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: REAL300025242047 none CC(CCNC(=O)[C@H]1OCCO[C@H]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 7, 12, 5, 5, 12, 5, 7, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 28, 28, 39, 39, 64, 104, 201, 201, 201, 201, 201, 19, 19, 19, 19, 15, 15, 12, 12, 4, 1, 1, 1, 1, 2, 2, 2, 28, 28, 28, 64, 64, 201] 201 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 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: 509 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242047 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242047 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242047/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242047 Building REAL300025242048 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242048' /scratch/stefan/7787021/working/building/REAL300025242048 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242048 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242048/0 /scratch/stefan/7787021/working/building/REAL300025242048 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/939 `/scratch/stefan/7787021/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC(=O)N(C)C=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242048.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242048 none CC(CCNC(=O)C1=CC(=O)N(C)C=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 5, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 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] 0 hydrogens 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, 112, 134, 169, 186, 200, 200, 200, 201, 201, 201, 201, 201, 201, 201, 76, 112, 29, 76, 13, 1, 1, 1, 1, 1, 1, 1, 134, 134, 134, 134, 169, 169, 186, 186, 200, 201, 201, 201, 201, 201, 112, 112, 112, 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: 809 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: REAL300025242048 none CC(CCNC(=O)C1=CC(=O)N(C)C=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 5, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 4, 7, 6, 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] 0 hydrogens 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, 12, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 18, 23, 23, 34, 34, 66, 104, 201, 201, 201, 201, 201, 18, 18, 18, 18, 13, 13, 8, 8, 3, 1, 2, 2, 2, 1, 23, 23, 23, 66, 66, 201] 201 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 40] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 513 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242048 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242048 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242048/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242048 Building REAL300025242049 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242049' /scratch/stefan/7787021/working/building/REAL300025242049 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242049 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242049/0 /scratch/stefan/7787021/working/building/REAL300025242049 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/940 `/scratch/stefan/7787021/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CNC(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=N1) `REAL300025242049.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242049 none CCC1=CNC(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 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, 7, 4, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 126, 126, 126, 126, 126, 71, 71, 71, 62, 62, 48, 43, 48, 32, 44, 24, 32, 13, 1, 1, 1, 1, 1, 1, 1, 126, 201, 201, 201, 201, 201, 126, 126, 126, 126, 71, 62, 62, 62, 62, 48, 48, 48, 48, 44, 44, 44, 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: 1017 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: REAL300025242049 none CCC1=CNC(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 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, 7, 4, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 4, 4, 4, 10, 10, 12, 12, 12, 12, 24, 24, 33, 54, 126, 126, 126, 126, 126, 1, 6, 6, 6, 6, 6, 1, 1, 3, 3, 4, 10, 10, 10, 10, 12, 12, 12, 12, 12, 12, 12, 33, 33, 126] 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, 49, 50]) total number of confs: 317 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242049 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242049 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242049/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242049 Building REAL300025242050 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242050' /scratch/stefan/7787021/working/building/REAL300025242050 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025242050 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242050/0 /scratch/stefan/7787021/working/building/REAL300025242050 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/941 `/scratch/stefan/7787021/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1CCC[N@@H+]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242050.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242050 none CC(CCNC(=O)CCC1CCC[N@@H+]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 9, 6, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [44, 36, 44, 47, 47, 50, 50, 50, 53, 53, 53, 53, 53, 53, 53, 53, 36, 36, 22, 35, 12, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 47, 47, 47, 47, 50, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 36, 36, 36, 22, 22, 1] 53 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: 205 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: REAL300025242050 none CC(CCNC(=O)CCC1CCC[N@@H+]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 9, 6, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [9, 8, 9, 7, 7, 3, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 11, 11, 11, 11, 20, 27, 53, 53, 53, 53, 53, 9, 9, 9, 9, 9, 9, 9, 9, 7, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 20, 20, 53] 53 rigid atoms, others: [45, 43, 15, 8, 9, 10, 11, 12, 13, 46, 44, 14, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 145 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242050 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025242050/1 /scratch/stefan/7787021/working/building/REAL300025242050 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/942 `/scratch/stefan/7787021/working/3D/942' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1CCC[N@H+]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242050.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025242050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242050/1/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: REAL300025242050 none CC(CCNC(=O)CCC1CCC[N@H+]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 9, 6, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 84, 92, 104, 117, 158, 158, 158, 200, 169, 201, 201, 201, 201, 201, 201, 73, 84, 32, 72, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 104, 104, 117, 117, 158, 200, 200, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 84, 84, 84, 32, 32, 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: 999 number of broken/clashed sets: 132 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242050 none CC(CCNC(=O)CCC1CCC[N@H+]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 9, 6, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 12, 12, 5, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 25, 27, 27, 32, 32, 68, 112, 201, 201, 201, 201, 201, 25, 25, 25, 25, 24, 24, 21, 21, 12, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 27, 27, 27, 68, 68, 201] 201 rigid atoms, others: [45, 43, 15, 8, 9, 10, 11, 12, 13, 46, 44, 14, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 544 number of broken/clashed sets: 132 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242050 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242050 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242050/0.* 1: /scratch/stefan/7787021/working/building/REAL300025242050/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242050 Building REAL300025242051 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242051' /scratch/stefan/7787021/working/building/REAL300025242051 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242051 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242051/0 /scratch/stefan/7787021/working/building/REAL300025242051 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/943 `/scratch/stefan/7787021/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CCNC1=O) `REAL300025242051.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242051 none CCC1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CCNC1=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.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 125, 100, 86, 100, 55, 86, 27, 54, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 143, 143, 125, 125, 100, 100, 100, 100, 86, 86, 86, 27, 27, 1, 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]) total number of confs: 797 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: REAL300025242051 none CCC1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CCNC1=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.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 8, 11, 18, 18, 29, 29, 49, 49, 73, 113, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 8, 11, 11, 18, 18, 18, 18, 29, 29, 29, 73, 73, 201, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 47, 48, 49, 50, 51, 22, 23, 24, 25, 26] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 531 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242051 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242051 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242051/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242051 Building REAL300025242052 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242052' /scratch/stefan/7787021/working/building/REAL300025242052 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242052 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242052/0 /scratch/stefan/7787021/working/building/REAL300025242052 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/944 `/scratch/stefan/7787021/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242052.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242052 none CC[C@@H]1CCO[C@@H]1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens need 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, 201, 201, 201, 174, 156, 132, 109, 132, 64, 109, 28, 64, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 174, 174, 156, 156, 132, 132, 132, 132, 109, 109, 109, 28, 28, 1] 201 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: 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: REAL300025242052 none CC[C@@H]1CCO[C@@H]1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 2, 2, 2, 7, 10, 16, 16, 25, 25, 40, 40, 68, 104, 201, 201, 201, 201, 201, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 7, 7, 10, 10, 16, 16, 16, 16, 25, 25, 25, 68, 68, 201] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36, 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, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 524 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242052 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242052 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242052/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242052 Building REAL300025242053 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242053' /scratch/stefan/7787021/working/building/REAL300025242053 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025242053 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242053/0 /scratch/stefan/7787021/working/building/REAL300025242053 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/945 `/scratch/stefan/7787021/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)[C@@H]1C[C@H]1C1=CNC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242053.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242053 none CC(CCNC(=O)[C@@H]1C[C@H]1C1=CNC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 37, 34, 21, 21, 8, 21, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 42, 46, 46, 48, 48, 86, 117, 201, 201, 201, 201, 201, 42, 42, 42, 42, 37, 37, 34, 34, 21, 8, 8, 1, 1, 1, 46, 46, 46, 86, 86, 201] 201 rigid atoms, others: [40, 41, 10, 12, 13, 14, 15, 16, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48]) total number of confs: 606 number of broken/clashed sets: 149 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242053 none CC(CCNC(=O)[C@@H]1C[C@H]1C1=CNC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 62, 68, 86, 103, 109, 109, 109, 201, 201, 201, 201, 201, 201, 201, 201, 201, 60, 62, 27, 60, 12, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 86, 86, 103, 103, 109, 201, 201, 201, 201, 201, 62, 62, 62, 27, 27, 1] 201 rigid atoms, others: [48, 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]) total number of confs: 759 number of broken/clashed sets: 149 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242053 none CC(CCNC(=O)[C@@H]1C[C@H]1C1=CNC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 18, 15, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 22, 25, 25, 27, 27, 63, 96, 201, 201, 201, 201, 201, 22, 22, 22, 22, 18, 18, 15, 15, 8, 1, 1, 8, 8, 8, 25, 25, 25, 63, 63, 201] 201 rigid atoms, others: [11, 5, 38, 7, 8, 9, 10, 39, 12] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 544 number of broken/clashed sets: 149 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242053 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025242053/1 /scratch/stefan/7787021/working/building/REAL300025242053 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/946 `/scratch/stefan/7787021/working/3D/946' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)[C@@H]1C[C@H]1C1=CN=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242053.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025242053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242053/1/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: REAL300025242053 none CC(CCNC(=O)[C@@H]1C[C@H]1C1=CN=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 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: [26, 25, 21, 17, 17, 4, 17, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 26, 26, 26, 27, 27, 67, 106, 201, 201, 201, 201, 201, 26, 26, 26, 26, 25, 25, 21, 21, 17, 4, 4, 1, 1, 1, 26, 26, 26, 67, 67, 201] 201 rigid atoms, others: [40, 41, 10, 12, 13, 14, 15, 16, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48]) total number of confs: 511 number of broken/clashed sets: 149 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242053 none CC(CCNC(=O)[C@@H]1C[C@H]1C1=CN=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 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: [49, 49, 49, 57, 66, 68, 68, 68, 161, 161, 161, 161, 161, 201, 201, 201, 201, 49, 49, 23, 49, 13, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 57, 57, 66, 66, 68, 161, 161, 201, 201, 201, 49, 49, 49, 23, 23, 1] 201 rigid atoms, others: [48, 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]) total number of confs: 593 number of broken/clashed sets: 149 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242053 none CC(CCNC(=O)[C@@H]1C[C@H]1C1=CN=CN1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 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: [17, 16, 13, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 17, 17, 17, 18, 18, 46, 73, 161, 161, 161, 161, 161, 17, 17, 17, 17, 16, 16, 13, 13, 10, 1, 1, 4, 4, 4, 17, 17, 17, 46, 46, 161] 201 rigid atoms, others: [11, 5, 38, 7, 8, 9, 10, 39, 12] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 377 number of broken/clashed sets: 149 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242053 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242053 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242053/0.* 1: /scratch/stefan/7787021/working/building/REAL300025242053/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242053 Building REAL300025242054 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242054' /scratch/stefan/7787021/working/building/REAL300025242054 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242054 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242054/0 /scratch/stefan/7787021/working/building/REAL300025242054 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/947 `/scratch/stefan/7787021/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCC=CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242054.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242054 none CC(CCNC(=O)C1CCC=CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [107, 94, 107, 110, 115, 115, 115, 115, 201, 201, 201, 201, 201, 201, 201, 70, 94, 27, 69, 13, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 110, 110, 115, 115, 115, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 94, 94, 94, 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: 685 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: REAL300025242054 none CC(CCNC(=O)C1CCC=CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [24, 16, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 24, 29, 29, 33, 33, 67, 111, 201, 201, 201, 201, 201, 24, 24, 24, 24, 18, 18, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 67, 67, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 49, 50, 51, 52, 53, 54]) total number of confs: 530 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242054 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242054 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242054/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242054 Building REAL300025242055 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242055' /scratch/stefan/7787021/working/building/REAL300025242055 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242055 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242055/0 /scratch/stefan/7787021/working/building/REAL300025242055 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/948 `/scratch/stefan/7787021/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1C(C)C1C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242055.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242055 none CC(CCNC(=O)C1C(C)C1C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 22, 20, 11, 11, 4, 11, 4, 4, 4, 1, 1, 1, 1, 30, 30, 30, 35, 35, 72, 107, 201, 201, 201, 201, 201, 30, 30, 30, 30, 23, 23, 20, 20, 11, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 30, 30, 30, 72, 72, 201] 201 rigid atoms, others: [45, 43, 41, 42, 11, 12, 13, 44, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 49, 50, 51]) total number of confs: 543 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242055 none CC(CCNC(=O)C1C(C)C1C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 73, 74, 84, 96, 107, 107, 107, 188, 188, 188, 188, 201, 201, 61, 73, 27, 60, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 84, 84, 96, 96, 107, 188, 188, 188, 188, 188, 188, 201, 201, 201, 201, 201, 73, 73, 73, 27, 27, 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: 755 number of broken/clashed sets: 120 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242055 none CC(CCNC(=O)C1C(C)C1C1CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 14, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 4, 4, 21, 21, 21, 26, 26, 53, 82, 188, 188, 188, 188, 188, 21, 21, 21, 21, 15, 15, 12, 12, 5, 1, 1, 2, 2, 2, 1, 4, 4, 4, 4, 4, 21, 21, 21, 53, 53, 188] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 469 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242055 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242055 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242055/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242055 Building REAL300025242056 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242056' /scratch/stefan/7787021/working/building/REAL300025242056 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242056 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242056/0 /scratch/stefan/7787021/working/building/REAL300025242056 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/949 `/scratch/stefan/7787021/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1(C)CCNC(=O)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242056.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242056 none CC(CCNC(=O)C1(C)CCNC(=O)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 111, 124, 146, 154, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 75, 111, 28, 75, 13, 1, 1, 1, 1, 1, 1, 1, 124, 124, 124, 124, 146, 146, 154, 154, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 111, 111, 111, 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: 760 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: REAL300025242056 none CC(CCNC(=O)C1(C)CCNC(=O)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 15, 22, 22, 30, 30, 63, 104, 201, 201, 201, 201, 201, 15, 15, 15, 15, 11, 11, 9, 9, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 63, 63, 201] 201 rigid atoms, others: [45, 11, 5, 7, 8, 9, 10, 39, 12, 13, 14, 44, 40, 43, 41, 42] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 49, 50, 51]) total number of confs: 513 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242056 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242056 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242056/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242056 Building REAL300025242057 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242057' /scratch/stefan/7787021/working/building/REAL300025242057 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242057 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242057/0 /scratch/stefan/7787021/working/building/REAL300025242057 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/950 `/scratch/stefan/7787021/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCCC12CC2)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242057.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242057 none CC(CCNC(=O)C1CCCC12CC2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 83, 99, 116, 123, 124, 124, 124, 201, 201, 201, 201, 201, 201, 61, 83, 30, 60, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 99, 116, 116, 123, 123, 124, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 83, 83, 83, 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: 799 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242057 none CC(CCNC(=O)C1CCCC12CC2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 12, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 18, 23, 23, 31, 31, 61, 100, 201, 201, 201, 201, 201, 18, 18, 18, 18, 13, 13, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 61, 61, 201] 201 rigid atoms, others: [45, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 43, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 46, 47, 48, 49, 50, 51]) total number of confs: 498 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242057 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242057 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242057/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242057 Building REAL300025242058 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242058' /scratch/stefan/7787021/working/building/REAL300025242058 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242058 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242058/0 /scratch/stefan/7787021/working/building/REAL300025242058 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/951 `/scratch/stefan/7787021/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CCCC1(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242058.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242058 none CCC1CCCC1(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 97, 201, 97, 97, 94, 90, 81, 69, 81, 48, 69, 26, 48, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 97, 94, 94, 90, 90, 81, 81, 81, 81, 69, 69, 69, 26, 26, 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: 715 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242058 none CCC1CCCC1(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 5, 5, 5, 13, 13, 19, 19, 24, 24, 30, 30, 60, 100, 201, 201, 201, 201, 201, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 13, 13, 15, 15, 19, 19, 19, 19, 24, 24, 24, 60, 60, 201] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 7, 34, 35, 36, 38, 37] set([0, 9, 10, 11, 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, 51, 52, 53, 54, 55, 56]) total number of confs: 515 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242058 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242058 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242058/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242058 Building REAL300025242059 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242059' /scratch/stefan/7787021/working/building/REAL300025242059 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242059 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242059/0 /scratch/stefan/7787021/working/building/REAL300025242059 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/952 `/scratch/stefan/7787021/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242059.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242059 none COCCOCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 98, 98, 98, 98, 76, 65, 50, 65, 42, 45, 29, 42, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 98, 98, 98, 76, 76, 65, 65, 65, 65, 50, 50, 50, 29, 29, 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: 954 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242059 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242059 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242059/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242059 Building REAL300025242060 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242060' /scratch/stefan/7787021/working/building/REAL300025242060 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242060 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242060/0 /scratch/stefan/7787021/working/building/REAL300025242060 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/953 `/scratch/stefan/7787021/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1CCCCC1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242060.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242060 none CC(CCNC(=O)CC1CCCCC1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 65, 71, 85, 91, 93, 93, 93, 201, 201, 201, 201, 201, 201, 201, 50, 65, 26, 50, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 85, 85, 91, 91, 93, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 65, 65, 65, 26, 26, 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: 874 number of broken/clashed sets: 111 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242060 none CC(CCNC(=O)CC1CCCCC1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 15, 14, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 20, 21, 21, 28, 28, 56, 96, 201, 201, 201, 201, 201, 20, 20, 20, 20, 16, 16, 14, 14, 6, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 56, 56, 201] 201 rigid atoms, others: [45, 11, 49, 38, 7, 8, 9, 10, 39, 12, 13, 46, 44, 48, 40, 50, 14, 43, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 51, 52, 53, 54, 55, 56]) total number of confs: 495 number of broken/clashed sets: 111 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242060 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242060 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242060/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242060 Building REAL300025242061 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242061' /scratch/stefan/7787021/working/building/REAL300025242061 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242061 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242061/0 /scratch/stefan/7787021/working/building/REAL300025242061 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/954 `/scratch/stefan/7787021/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1=CC=CC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242061.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242061 none CC(CCNC(=O)CCC1=CC=CC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 72, 89, 113, 124, 127, 127, 127, 191, 201, 201, 201, 201, 201, 201, 54, 72, 27, 54, 12, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 113, 113, 124, 124, 127, 191, 191, 201, 201, 201, 201, 201, 201, 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: 915 number of broken/clashed sets: 144 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242061 none CC(CCNC(=O)CCC1=CC=CC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 14, 14, 9, 14, 6, 1, 1, 1, 1, 1, 1, 1, 22, 24, 24, 28, 28, 64, 101, 201, 201, 201, 201, 201, 22, 22, 22, 22, 19, 19, 18, 18, 14, 9, 9, 6, 6, 1, 1, 1, 1, 24, 24, 24, 64, 64, 201] 201 rigid atoms, others: [43, 8, 9, 10, 11, 12, 13, 14, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49]) total number of confs: 539 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242061 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242061 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242061/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242061 Building REAL300025242062 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242062' /scratch/stefan/7787021/working/building/REAL300025242062 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242062 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242062/0 /scratch/stefan/7787021/working/building/REAL300025242062 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/955 `/scratch/stefan/7787021/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1=CSC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242062.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242062 none CC(CCNC(=O)CCC1=CSC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 14, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [40, 40, 40, 47, 57, 68, 68, 68, 177, 184, 201, 201, 201, 201, 40, 40, 24, 39, 13, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 47, 47, 57, 57, 68, 177, 177, 184, 184, 201, 201, 40, 40, 40, 24, 24, 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: 763 number of broken/clashed sets: 147 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242062 none CC(CCNC(=O)CCC1=CSC=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 14, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [40, 38, 32, 22, 22, 6, 22, 4, 1, 1, 1, 1, 1, 1, 40, 40, 40, 41, 41, 79, 115, 201, 201, 201, 201, 201, 40, 40, 40, 40, 38, 38, 32, 32, 22, 6, 6, 4, 4, 1, 1, 40, 40, 40, 79, 79, 201] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 576 number of broken/clashed sets: 147 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242062 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242062 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242062/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242062 Building REAL300025242063 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242063' /scratch/stefan/7787021/working/building/REAL300025242063 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242063 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242063/0 /scratch/stefan/7787021/working/building/REAL300025242063 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/956 `/scratch/stefan/7787021/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCCN1C=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242063.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242063 none CC(CCNC(=O)CCCN1C=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [35, 35, 35, 35, 35, 35, 35, 35, 104, 95, 124, 201, 201, 201, 201, 28, 35, 14, 27, 10, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 104, 104, 124, 124, 124, 124, 201, 201, 201, 35, 35, 35, 14, 14, 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: 849 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: REAL300025242063 none CC(CCNC(=O)CCCN1C=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 26, 26, 26, 8, 26, 4, 4, 1, 1, 1, 1, 1, 1, 26, 26, 26, 29, 29, 68, 101, 201, 201, 201, 201, 201, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 4, 4, 4, 4, 1, 1, 1, 26, 26, 26, 68, 68, 201] 201 rigid atoms, others: [43, 9, 10, 11, 12, 13, 14, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47, 48, 49, 50]) total number of confs: 522 number of broken/clashed sets: 123 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242063 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242063 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242063/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242063 Building REAL300025242064 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242064' /scratch/stefan/7787021/working/building/REAL300025242064 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242064 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242064/0 /scratch/stefan/7787021/working/building/REAL300025242064 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/957 `/scratch/stefan/7787021/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242064.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242064 none CC(C)OCCCC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 201, 185, 128, 180, 64, 64, 64, 64, 64, 43, 42, 43, 31, 43, 22, 31, 11, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 151, 167, 180, 180, 180, 180, 64, 64, 64, 64, 64, 43, 43, 43, 43, 43, 43, 43, 22, 22, 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: 1111 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242064 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242064 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242064/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242064 Building REAL300025242065 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242065' /scratch/stefan/7787021/working/building/REAL300025242065 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242065 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242065/0 /scratch/stefan/7787021/working/building/REAL300025242065 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/958 `/scratch/stefan/7787021/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCCC(N)=O)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242065.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242065 none CC(CCNC(=O)CCCC(N)=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 73, 93, 94, 94, 94, 183, 152, 201, 201, 201, 61, 62, 31, 60, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 73, 73, 93, 93, 94, 183, 183, 186, 186, 178, 195, 201, 201, 62, 62, 62, 31, 31, 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: 1033 number of broken/clashed sets: 154 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242065 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242065 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242065/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242065 Building REAL300025242066 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242066' /scratch/stefan/7787021/working/building/REAL300025242066 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242066 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242066/0 /scratch/stefan/7787021/working/building/REAL300025242066 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/959 `/scratch/stefan/7787021/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CC[NH+](C)CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242066.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242066 none CC(CCNC(=O)C1CC[NH+](C)CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 93, 100, 139, 139, 167, 167, 167, 201, 201, 201, 201, 201, 201, 201, 79, 93, 30, 79, 13, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 139, 139, 139, 139, 167, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 93, 93, 93, 30, 30, 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: 784 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242066 none CC(CCNC(=O)C1CC[NH+](C)CC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 21, 25, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 25, 30, 30, 38, 38, 77, 121, 201, 201, 201, 201, 201, 25, 25, 25, 25, 25, 25, 25, 25, 9, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 30, 30, 30, 77, 77, 201] 201 rigid atoms, others: [45, 11, 36, 5, 38, 7, 8, 9, 10, 39, 12, 13, 14, 44, 40, 46, 47, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 48, 49, 50, 51, 52, 53]) total number of confs: 565 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242066 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242066 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242066/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242066 Building REAL300025242067 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242067' /scratch/stefan/7787021/working/building/REAL300025242067 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242067 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242067/0 /scratch/stefan/7787021/working/building/REAL300025242067 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/960 `/scratch/stefan/7787021/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)[C@@H]1CCCN1C(N)=O)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242067.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242067 none CC(CCNC(=O)[C@@H]1CCCN1C(N)=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 81, 88, 114, 151, 171, 171, 171, 197, 197, 197, 197, 197, 197, 201, 201, 64, 81, 27, 64, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 114, 114, 151, 151, 171, 197, 197, 197, 197, 197, 197, 201, 201, 81, 81, 81, 27, 27, 1] 201 rigid atoms, others: [50, 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]) total number of confs: 863 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242067 none CC(CCNC(=O)[C@@H]1CCCN1C(N)=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 14, 16, 16, 23, 23, 58, 93, 197, 197, 197, 197, 197, 14, 14, 14, 14, 11, 11, 7, 7, 3, 1, 1, 1, 1, 1, 1, 3, 3, 16, 16, 16, 58, 58, 197] 201 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 12, 13, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 504 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242067 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242067 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242067/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242067 Building REAL300025242068 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242068' /scratch/stefan/7787021/working/building/REAL300025242068 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242068 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242068/0 /scratch/stefan/7787021/working/building/REAL300025242068 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/961 `/scratch/stefan/7787021/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(F)=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242068.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242068 none CC1=CC=CC(F)=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 193, 201, 201, 201, 131, 131, 131, 130, 115, 98, 85, 98, 59, 85, 27, 59, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 131, 130, 130, 115, 115, 98, 98, 98, 98, 85, 85, 85, 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: 685 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242068 none CC1=CC=CC(F)=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 1, 1, 8, 8, 8, 14, 19, 26, 26, 33, 33, 43, 43, 78, 113, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 8, 14, 14, 19, 19, 26, 26, 26, 26, 33, 33, 33, 78, 78, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 30, 31] set([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: 584 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242068 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242068 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242068/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242068 Building REAL300025242069 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242069' /scratch/stefan/7787021/working/building/REAL300025242069 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242069 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242069/0 /scratch/stefan/7787021/working/building/REAL300025242069 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/962 `/scratch/stefan/7787021/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=NN1C) `REAL300025242069.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242069 none CCC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=NN1C 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 104, 104, 104, 104, 104, 104, 97, 95, 79, 60, 79, 50, 60, 35, 50, 13, 1, 1, 1, 1, 1, 1, 1, 104, 104, 104, 201, 201, 201, 201, 201, 104, 104, 97, 97, 95, 95, 79, 79, 79, 79, 60, 60, 60, 35, 35, 1, 104, 104, 104] 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]) total number of confs: 1026 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: REAL300025242069 none CCC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=NN1C 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 6, 10, 10, 13, 13, 25, 25, 33, 56, 104, 104, 104, 104, 104, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 5, 5, 6, 6, 10, 10, 10, 10, 13, 13, 13, 33, 33, 104, 2, 2, 2] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 33, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 270 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242069 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242069 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242069/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242069 Building REAL300025242070 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242070' /scratch/stefan/7787021/working/building/REAL300025242070 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242070 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242070/0 /scratch/stefan/7787021/working/building/REAL300025242070 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/963 `/scratch/stefan/7787021/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=C(C)C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=N1) `REAL300025242070.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242070 none CCN1N=C(C)C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 134, 134, 134, 134, 134, 129, 129, 129, 90, 90, 65, 55, 65, 41, 56, 29, 41, 12, 1, 1, 1, 1, 1, 1, 1, 134, 201, 201, 201, 201, 201, 134, 134, 134, 129, 90, 90, 90, 90, 65, 65, 65, 65, 56, 56, 56, 29, 29, 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: 938 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: REAL300025242070 none CCN1N=C(C)C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 9, 9, 13, 13, 16, 16, 30, 30, 40, 60, 134, 134, 134, 134, 134, 1, 6, 6, 6, 5, 5, 2, 2, 2, 4, 9, 9, 9, 9, 13, 13, 13, 13, 16, 16, 16, 40, 40, 134] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 26] set([0, 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, 48, 49]) total number of confs: 354 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242070 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242070 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242070/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242070 Building REAL300025242071 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242071' /scratch/stefan/7787021/working/building/REAL300025242071 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242071 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242071/0 /scratch/stefan/7787021/working/building/REAL300025242071 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/964 `/scratch/stefan/7787021/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1=CN(C)N=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242071.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242071 none CC(CCNC(=O)CCC1=CN(C)N=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 5, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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: [78, 76, 78, 88, 108, 118, 118, 118, 181, 186, 201, 201, 201, 201, 201, 59, 76, 29, 59, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 88, 88, 108, 108, 118, 181, 181, 186, 186, 201, 201, 201, 201, 76, 76, 76, 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: 830 number of broken/clashed sets: 140 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242071 none CC(CCNC(=O)CCC1=CN(C)N=N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 5, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 29, 28, 23, 23, 10, 23, 6, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 35, 35, 73, 111, 201, 201, 201, 201, 201, 32, 32, 32, 32, 29, 29, 28, 28, 23, 10, 10, 6, 6, 1, 2, 2, 2, 32, 32, 32, 73, 73, 201] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 556 number of broken/clashed sets: 140 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242071 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242071 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242071/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242071 Building REAL300025242072 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242072' /scratch/stefan/7787021/working/building/REAL300025242072 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242072 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242072/0 /scratch/stefan/7787021/working/building/REAL300025242072 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/965 `/scratch/stefan/7787021/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1CCCC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242072.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242072 none CCCC1CCCC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 151, 151, 151, 48, 48, 48, 46, 46, 33, 32, 33, 24, 33, 17, 24, 10, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 151, 151, 151, 151, 151, 151, 151, 151, 48, 46, 46, 46, 46, 33, 33, 33, 33, 33, 33, 33, 17, 17, 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: 772 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: REAL300025242072 none CCCC1CCCC1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 11, 29, 29, 40, 69, 151, 151, 151, 151, 151, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 40, 40, 151] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 40, 41, 39, 34, 8, 35, 36, 38, 37] 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 370 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242072 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242072 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242072/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242072 Building REAL300025242073 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242073' /scratch/stefan/7787021/working/building/REAL300025242073 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242073 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242073/0 /scratch/stefan/7787021/working/building/REAL300025242073 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/966 `/scratch/stefan/7787021/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)C(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242073.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242073 none CCC(CC)C(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 137, 137, 137, 201, 67, 137, 67, 67, 66, 62, 58, 53, 58, 43, 53, 22, 42, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 137, 201, 201, 201, 201, 201, 137, 137, 137, 137, 67, 66, 66, 62, 62, 58, 58, 58, 58, 53, 53, 53, 22, 22, 1] 201 rigid atoms, others: [55, 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, 51, 52, 53, 54]) total number of confs: 1352 number of broken/clashed sets: 115 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242073 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242073 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242073/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242073 Building REAL300025242074 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242074' /scratch/stefan/7787021/working/building/REAL300025242074 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242074 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242074/0 /scratch/stefan/7787021/working/building/REAL300025242074 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/967 `/scratch/stefan/7787021/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CN1N=CN(C)C1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242074.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242074 none CC(CCNC(=O)CN1N=CN(C)C1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 8, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [85, 75, 85, 102, 102, 117, 117, 117, 150, 201, 201, 201, 201, 201, 201, 68, 75, 27, 67, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 102, 102, 102, 102, 117, 150, 150, 201, 201, 201, 201, 75, 75, 75, 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: 738 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242074 none CC(CCNC(=O)CN1N=CN(C)C1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 8, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [18, 12, 15, 8, 8, 3, 8, 1, 1, 1, 1, 1, 1, 1, 1, 18, 21, 21, 24, 24, 57, 98, 201, 201, 201, 201, 201, 18, 18, 18, 18, 15, 15, 15, 15, 8, 3, 3, 1, 2, 2, 2, 21, 21, 21, 57, 57, 201] 201 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 505 number of broken/clashed sets: 113 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242074 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242074 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242074/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242074 Building REAL300025242075 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242075' /scratch/stefan/7787021/working/building/REAL300025242075 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242075 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242075/0 /scratch/stefan/7787021/working/building/REAL300025242075 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/968 `/scratch/stefan/7787021/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CN=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242075.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242075 none CCC1=CN=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 118, 118, 118, 74, 118, 118, 70, 70, 70, 68, 64, 61, 60, 61, 49, 60, 25, 48, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 118, 118, 118, 70, 68, 68, 64, 64, 61, 61, 61, 61, 60, 60, 60, 25, 25, 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: 962 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242075 none CCC1=CN=CC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 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, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 13, 15, 18, 18, 18, 18, 20, 20, 38, 58, 118, 118, 118, 118, 118, 3, 3, 3, 3, 3, 1, 1, 1, 7, 13, 13, 15, 15, 18, 18, 18, 18, 18, 18, 18, 38, 38, 118] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33] set([0, 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: 313 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242075 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242075 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242075/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242075 Building REAL300025242076 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242076' /scratch/stefan/7787021/working/building/REAL300025242076 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242076 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242076/0 /scratch/stefan/7787021/working/building/REAL300025242076 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/969 `/scratch/stefan/7787021/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1(F)CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242076.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242076 none CC(CCNC(=O)C1(F)CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 84, 97, 108, 125, 126, 126, 126, 201, 201, 201, 201, 201, 57, 84, 28, 57, 13, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 97, 108, 108, 125, 125, 126, 201, 201, 201, 201, 201, 201, 201, 201, 84, 84, 84, 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: 785 number of broken/clashed sets: 99 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242076 none CC(CCNC(=O)C1(F)CCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 17, 12, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 24, 29, 29, 40, 40, 80, 121, 201, 201, 201, 201, 201, 24, 24, 24, 24, 17, 17, 12, 12, 7, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 80, 80, 201] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45, 46, 47]) total number of confs: 585 number of broken/clashed sets: 99 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242076 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242076 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242076/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242076 Building REAL300025242077 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242077' /scratch/stefan/7787021/working/building/REAL300025242077 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242077 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242077/0 /scratch/stefan/7787021/working/building/REAL300025242077 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/970 `/scratch/stefan/7787021/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CN=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242077.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242077 none CCC1=CC=CN=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 183, 183, 183, 183, 183, 98, 98, 98, 97, 86, 68, 56, 68, 41, 56, 27, 41, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 183, 183, 183, 98, 97, 97, 86, 86, 68, 68, 68, 68, 56, 56, 56, 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: 681 number of broken/clashed sets: 119 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242077 none CCC1=CC=CN=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 10, 14, 19, 19, 24, 24, 32, 32, 64, 96, 183, 183, 183, 183, 183, 3, 3, 3, 3, 3, 1, 1, 1, 5, 10, 10, 14, 14, 19, 19, 19, 19, 24, 24, 24, 64, 64, 183] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33] set([0, 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: 507 number of broken/clashed sets: 119 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242077 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242077 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242077/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242077 Building REAL300025242078 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242078' /scratch/stefan/7787021/working/building/REAL300025242078 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242078 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242078/0 /scratch/stefan/7787021/working/building/REAL300025242078 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/971 `/scratch/stefan/7787021/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C(=O)NCC(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242078.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242078 none CC(CCNC(=O)C(=O)NCC(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 4, 7, 6, 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: [48, 47, 48, 64, 78, 102, 102, 102, 102, 102, 102, 201, 201, 201, 42, 47, 26, 41, 13, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 64, 64, 78, 78, 102, 102, 201, 201, 201, 47, 47, 47, 26, 26, 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: 937 number of broken/clashed sets: 143 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242078 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242078 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242078/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242078 Building REAL300025242079 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242079' /scratch/stefan/7787021/working/building/REAL300025242079 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242079 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242079/0 /scratch/stefan/7787021/working/building/REAL300025242079 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/972 `/scratch/stefan/7787021/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CN(CCF)N=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242079.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242079 none CC(CCNC(=O)C1=CN(CCF)N=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 15, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [95, 95, 95, 95, 95, 95, 95, 95, 142, 142, 142, 201, 201, 142, 142, 81, 95, 30, 81, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 95, 95, 95, 95, 95, 142, 201, 201, 201, 201, 142, 95, 95, 95, 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: 718 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: REAL300025242079 none CC(CCNC(=O)C1=CN(CCF)N=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 15, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 6, 8, 1, 1, 5, 5, 5, 7, 7, 22, 44, 142, 142, 142, 142, 142, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 6, 6, 8, 8, 1, 5, 5, 5, 22, 22, 142] 201 rigid atoms, others: [36, 5, 7, 8, 9, 10, 13, 14, 41] set([0, 1, 2, 3, 4, 6, 11, 12, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 281 number of broken/clashed sets: 110 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242079 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242079 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242079/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242079 Building REAL300025242080 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242080' /scratch/stefan/7787021/working/building/REAL300025242080 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242080 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242080/0 /scratch/stefan/7787021/working/building/REAL300025242080 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/973 `/scratch/stefan/7787021/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=NC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1) `REAL300025242080.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242080 none CC1=CC(C)=NC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens need 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, 201, 182, 159, 122, 109, 122, 67, 109, 29, 67, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 182, 182, 159, 159, 122, 122, 122, 122, 109, 109, 109, 29, 29, 1, 201] 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, 49]) total number of confs: 841 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: REAL300025242080 none CC1=CC(C)=NC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 3, 3, 3, 9, 10, 19, 19, 28, 28, 38, 38, 67, 105, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 2, 2, 2, 3, 9, 9, 11, 11, 19, 19, 19, 19, 28, 28, 28, 67, 67, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 49, 26, 30] set([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: 526 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242080 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242080 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242080/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242080 Building REAL300025242081 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242081' /scratch/stefan/7787021/working/building/REAL300025242081 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242081 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242081/0 /scratch/stefan/7787021/working/building/REAL300025242081 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/974 `/scratch/stefan/7787021/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CN=CN1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242081.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242081 none CC(CCNC(=O)C1=CN=CN1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [113, 96, 113, 143, 165, 188, 188, 188, 201, 201, 201, 201, 201, 63, 96, 27, 63, 13, 1, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 143, 143, 165, 165, 188, 201, 201, 201, 201, 201, 96, 96, 96, 27, 27, 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: 791 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: REAL300025242081 none CC(CCNC(=O)C1=CN=CN1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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: [18, 13, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 18, 24, 24, 35, 35, 64, 103, 201, 201, 201, 201, 201, 18, 18, 18, 18, 13, 13, 9, 9, 4, 1, 1, 2, 2, 2, 24, 24, 24, 64, 64, 201] 201 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 521 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242081 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242081 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242081/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242081 Building REAL300025242082 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242082' /scratch/stefan/7787021/working/building/REAL300025242082 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242082 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242082/0 /scratch/stefan/7787021/working/building/REAL300025242082 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/975 `/scratch/stefan/7787021/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1=CC=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242082.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242082 none CC(CCNC(=O)CCC1=CC=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 53, 56, 56, 61, 62, 62, 62, 143, 145, 201, 201, 201, 201, 201, 44, 53, 21, 43, 13, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 56, 61, 61, 62, 143, 143, 145, 145, 201, 201, 201, 201, 53, 53, 53, 21, 21, 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: 658 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242082 none CC(CCNC(=O)CCC1=CC=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 23, 23, 6, 23, 3, 1, 1, 1, 1, 1, 1, 1, 29, 30, 30, 31, 31, 68, 107, 201, 201, 201, 201, 201, 29, 29, 29, 29, 29, 29, 27, 27, 23, 6, 6, 3, 3, 1, 1, 1, 1, 30, 30, 30, 68, 68, 201] 201 rigid atoms, others: [43, 8, 9, 10, 11, 12, 13, 14, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49]) total number of confs: 522 number of broken/clashed sets: 136 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242082 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242082 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242082/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242082 Building REAL300025242083 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242083' /scratch/stefan/7787021/working/building/REAL300025242083 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242083 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242083/0 /scratch/stefan/7787021/working/building/REAL300025242083 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/976 `/scratch/stefan/7787021/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C(C)S1) `REAL300025242083.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242083 none CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 137, 127, 112, 94, 112, 68, 94, 27, 68, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 137, 137, 137, 127, 127, 112, 112, 112, 112, 94, 94, 94, 27, 27, 1, 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]) total number of confs: 659 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: REAL300025242083 none CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 12, 20, 20, 26, 26, 34, 34, 74, 123, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 5, 10, 10, 13, 13, 20, 20, 20, 20, 26, 26, 26, 74, 74, 201, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 558 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242083 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242083 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242083/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242083 Building REAL300025242084 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242084' /scratch/stefan/7787021/working/building/REAL300025242084 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242084 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242084/0 /scratch/stefan/7787021/working/building/REAL300025242084 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/977 `/scratch/stefan/7787021/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)S1) `REAL300025242084.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242084 none CCC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)S1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 112, 112, 112, 112, 111, 111, 111, 102, 102, 84, 62, 84, 50, 63, 32, 50, 13, 1, 1, 1, 1, 1, 1, 1, 112, 201, 201, 201, 201, 201, 112, 112, 111, 102, 102, 102, 102, 84, 84, 84, 84, 63, 63, 63, 32, 32, 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: 1017 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242084 none CCC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)S1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 8, 8, 10, 10, 13, 13, 25, 25, 36, 56, 112, 112, 112, 112, 112, 1, 3, 3, 3, 3, 3, 1, 1, 3, 8, 8, 8, 8, 10, 10, 10, 10, 13, 13, 13, 36, 36, 112] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 290 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242084 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242084 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242084/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242084 Building REAL300025242085 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242085' /scratch/stefan/7787021/working/building/REAL300025242085 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242085 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242085/0 /scratch/stefan/7787021/working/building/REAL300025242085 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/978 `/scratch/stefan/7787021/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=C1) `REAL300025242085.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242085 none CC1=CC=C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 113, 113, 113, 97, 96, 76, 59, 76, 47, 60, 33, 47, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 113, 97, 97, 96, 96, 76, 76, 76, 76, 60, 60, 60, 33, 33, 1, 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]) total number of confs: 875 number of broken/clashed sets: 89 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242085 none CC1=CC=C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 7, 7, 7, 15, 16, 21, 21, 22, 22, 45, 45, 62, 99, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 5, 5, 7, 15, 15, 16, 16, 21, 21, 21, 21, 22, 22, 22, 62, 62, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 49, 50, 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, 47, 48]) total number of confs: 520 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242085 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242085 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242085/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242085 Building REAL300025242086 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242086' /scratch/stefan/7787021/working/building/REAL300025242086 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242086 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242086/0 /scratch/stefan/7787021/working/building/REAL300025242086 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/979 `/scratch/stefan/7787021/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)SN=N1) `REAL300025242086.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242086 none CCC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)SN=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.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, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 8, 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, 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, 7, 7, 7] 0 hydrogens need 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, 145, 145, 145, 144, 128, 112, 106, 112, 76, 106, 30, 76, 12, 1, 1, 1, 1, 1, 1, 1, 165, 165, 165, 201, 201, 201, 201, 201, 145, 144, 144, 128, 128, 112, 112, 112, 112, 106, 106, 106, 30, 30, 1] 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]) total number of confs: 814 number of broken/clashed sets: 122 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242086 none CCC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)SN=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.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, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 8, 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, 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, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 7, 8, 12, 12, 14, 14, 20, 20, 49, 75, 165, 165, 165, 165, 165, 1, 1, 1, 5, 5, 5, 4, 4, 3, 7, 7, 8, 8, 12, 12, 12, 12, 14, 14, 14, 49, 49, 165] 201 rigid atoms, others: [1, 2, 3, 4, 23, 24, 25] set([0, 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: 410 number of broken/clashed sets: 122 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242086 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242086 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242086/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242086 Building REAL300025242087 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242087' /scratch/stefan/7787021/working/building/REAL300025242087 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242087 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242087/0 /scratch/stefan/7787021/working/building/REAL300025242087 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/980 `/scratch/stefan/7787021/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C(C)C(C)(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242087.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242087 none CC(CCNC(=O)C(C)C(C)(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 119, 137, 173, 188, 190, 190, 190, 201, 201, 201, 201, 201, 78, 119, 30, 77, 13, 1, 1, 1, 1, 1, 1, 1, 137, 137, 137, 137, 173, 173, 188, 188, 190, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 119, 119, 119, 30, 30, 1] 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]) total number of confs: 833 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242087 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242087 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242087/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242087 Building REAL300025242088 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242088' /scratch/stefan/7787021/working/building/REAL300025242088 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242088 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242088/0 /scratch/stefan/7787021/working/building/REAL300025242088 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/981 `/scratch/stefan/7787021/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C12CCC(CC1)C2)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242088.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242088 none CC(CCNC(=O)C12CCC(CC1)C2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 60, 70, 76, 80, 80, 80, 80, 201, 201, 201, 201, 201, 201, 46, 60, 24, 45, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 76, 76, 80, 80, 80, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 60, 60, 60, 24, 24, 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: 480 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242088 none CC(CCNC(=O)C12CCC(CC1)C2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 11, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 17, 23, 23, 27, 27, 55, 94, 201, 201, 201, 201, 201, 17, 17, 17, 17, 11, 11, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 55, 55, 201] 201 rigid atoms, others: [45, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 43, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 46, 47, 48, 49, 50, 51]) total number of confs: 480 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242088 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242088 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242088/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242088 Building REAL300025242089 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242089' /scratch/stefan/7787021/working/building/REAL300025242089 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300025242089 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242089/0 /scratch/stefan/7787021/working/building/REAL300025242089 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/982 `/scratch/stefan/7787021/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCCC[N@@H+]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242089.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242089 none CC(CCNC(=O)C1CCCC[N@@H+]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 95, 97, 128, 129, 169, 169, 169, 201, 201, 201, 201, 201, 201, 201, 79, 95, 32, 79, 13, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 97, 128, 128, 129, 129, 169, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 95, 95, 95, 32, 32, 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: 759 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: REAL300025242089 none CC(CCNC(=O)C1CCCC[N@@H+]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 23, 26, 26, 33, 33, 69, 111, 201, 201, 201, 201, 201, 23, 23, 23, 23, 20, 20, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 26, 26, 26, 69, 69, 201] 201 rigid atoms, others: [11, 36, 5, 38, 7, 8, 9, 10, 39, 12, 13, 14, 44, 40, 43, 41, 42, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 540 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242089 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025242089/1 /scratch/stefan/7787021/working/building/REAL300025242089 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/983 `/scratch/stefan/7787021/working/3D/983' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCCC[N@H+]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242089.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025242089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242089/1/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: REAL300025242089 none CC(CCNC(=O)C1CCCC[N@H+]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 106, 119, 151, 151, 187, 187, 187, 201, 201, 201, 201, 201, 201, 201, 92, 106, 34, 92, 13, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 151, 151, 151, 151, 187, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 106, 106, 34, 34, 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: 785 number of broken/clashed sets: 117 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242089 none CC(CCNC(=O)C1CCCC[N@H+]1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 20, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 20, 24, 24, 31, 31, 70, 114, 201, 201, 201, 201, 201, 20, 20, 20, 20, 20, 20, 20, 20, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 24, 24, 24, 70, 70, 201] 201 rigid atoms, others: [11, 36, 5, 38, 7, 8, 9, 10, 39, 12, 13, 14, 44, 40, 43, 41, 42, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 534 number of broken/clashed sets: 117 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242089 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `2' /scratch/stefan/7787021/working/building/REAL300025242089/2 /scratch/stefan/7787021/working/building/REAL300025242089 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 2 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/984 `/scratch/stefan/7787021/working/3D/984' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCCCN1C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242089.mol2' -> `2.mol2' `temp.mol2' -> `REAL300025242089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242089/2/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: REAL300025242089 none CC(CCNC(=O)C1CCCCN1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 10, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 109, 125, 163, 189, 201, 201, 201, 201, 201, 201, 201, 201, 201, 63, 109, 28, 63, 13, 1, 1, 1, 1, 1, 1, 1, 125, 125, 125, 125, 163, 163, 189, 189, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 109, 109, 109, 28, 28, 1] 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]) total number of confs: 845 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: REAL300025242089 none CC(CCNC(=O)C1CCCCN1C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 10, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7] 0 hydrogens 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, 8, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 13, 21, 21, 36, 36, 71, 105, 201, 201, 201, 201, 201, 13, 13, 13, 13, 8, 8, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 21, 21, 71, 71, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 39, 12, 13, 11, 40, 43, 41, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 514 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242089 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242089 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242089/0.* 1: /scratch/stefan/7787021/working/building/REAL300025242089/1.* 2: /scratch/stefan/7787021/working/building/REAL300025242089/2.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242089 Building REAL300025242090 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242090' /scratch/stefan/7787021/working/building/REAL300025242090 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242090 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242090/0 /scratch/stefan/7787021/working/building/REAL300025242090 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/985 `/scratch/stefan/7787021/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C(C)S(C)(=O)=O)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242090.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242090 none CC(CCNC(=O)C(C)S(C)(=O)=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 14, 5, 11, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 66, 73, 87, 118, 160, 160, 160, 201, 201, 201, 201, 201, 55, 66, 27, 54, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73, 87, 87, 118, 118, 160, 201, 201, 201, 201, 201, 201, 201, 66, 66, 66, 27, 27, 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: 918 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242090 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242090 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242090/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242090 Building REAL300025242091 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242091' /scratch/stefan/7787021/working/building/REAL300025242091 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242091 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242091/0 /scratch/stefan/7787021/working/building/REAL300025242091 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/986 `/scratch/stefan/7787021/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCS(C)(=O)=O)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242091.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242091 none CC(CCNC(=O)CCS(C)(=O)=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 14, 5, 11, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 62, 73, 87, 119, 142, 142, 142, 198, 201, 201, 201, 201, 55, 62, 24, 54, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73, 87, 87, 119, 119, 142, 198, 198, 201, 201, 201, 201, 201, 62, 62, 62, 24, 24, 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: 936 number of broken/clashed sets: 125 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242091 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242091 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242091/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242091 Building REAL300025242092 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242092' /scratch/stefan/7787021/working/building/REAL300025242092 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242092 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242092/0 /scratch/stefan/7787021/working/building/REAL300025242092 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/987 `/scratch/stefan/7787021/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1=CC=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242092.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242092 none CC(CCNC(=O)CC1=CC=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [59, 58, 59, 59, 59, 63, 63, 63, 152, 201, 201, 201, 201, 201, 49, 58, 24, 48, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 63, 152, 152, 201, 201, 201, 201, 58, 58, 58, 24, 24, 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: 687 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242092 none CC(CCNC(=O)CC1=CC=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 14, 15, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 21, 21, 54, 91, 201, 201, 201, 201, 201, 15, 15, 15, 15, 15, 15, 15, 15, 9, 3, 3, 1, 1, 1, 1, 15, 15, 15, 54, 54, 201] 201 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 13, 40, 39] 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, 41, 42, 43, 44, 45, 46]) total number of confs: 478 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242092 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242092 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242092/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242092 Building REAL300025242093 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242093' /scratch/stefan/7787021/working/building/REAL300025242093 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242093 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242093/0 /scratch/stefan/7787021/working/building/REAL300025242093 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/988 `/scratch/stefan/7787021/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)O1) `REAL300025242093.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242093 none CCC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 119, 117, 117, 117, 86, 86, 60, 50, 60, 40, 51, 26, 40, 12, 1, 1, 1, 1, 1, 1, 1, 119, 201, 201, 201, 201, 201, 119, 119, 117, 86, 86, 86, 86, 60, 60, 60, 60, 51, 51, 51, 26, 26, 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: 982 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242093 none CCC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 8, 8, 12, 12, 15, 15, 24, 24, 31, 51, 119, 119, 119, 119, 119, 1, 7, 7, 7, 7, 7, 1, 1, 3, 8, 8, 8, 8, 12, 12, 12, 12, 15, 15, 15, 31, 31, 119] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 293 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242093 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242093 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242093/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242093 Building REAL300025242094 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242094' /scratch/stefan/7787021/working/building/REAL300025242094 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242094 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242094/0 /scratch/stefan/7787021/working/building/REAL300025242094 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/989 `/scratch/stefan/7787021/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCN(C)C(=O)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242094.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242094 none CC(CCNC(=O)C1CCN(C)C(=O)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 5, 1, 11, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 102, 110, 115, 120, 122, 122, 122, 201, 201, 201, 201, 201, 201, 201, 75, 102, 30, 74, 13, 1, 1, 1, 1, 1, 1, 1, 110, 110, 110, 110, 115, 115, 120, 120, 122, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 102, 102, 102, 30, 30, 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: 692 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: REAL300025242094 none CC(CCNC(=O)C1CCN(C)C(=O)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 5, 1, 11, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 19, 22, 22, 30, 30, 69, 114, 201, 201, 201, 201, 201, 19, 19, 19, 19, 15, 15, 14, 14, 9, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 22, 22, 22, 69, 69, 201] 201 rigid atoms, others: [45, 11, 36, 5, 38, 7, 8, 9, 10, 39, 12, 13, 14, 44, 40, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47, 48, 49, 50, 51]) total number of confs: 523 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242094 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242094 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242094/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242094 Building REAL300025242095 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242095' /scratch/stefan/7787021/working/building/REAL300025242095 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242095 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242095/0 /scratch/stefan/7787021/working/building/REAL300025242095 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/990 `/scratch/stefan/7787021/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC(=O)N(C)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242095.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242095 none CC(CCNC(=O)C1=CC(=O)N(C)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 5, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 65, 79, 82, 86, 86, 86, 86, 201, 201, 201, 201, 201, 201, 201, 55, 65, 27, 54, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 82, 82, 86, 86, 86, 201, 201, 201, 201, 201, 201, 65, 65, 65, 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: 512 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242095 none CC(CCNC(=O)C1=CC(=O)N(C)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 5, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 13, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 18, 23, 23, 27, 27, 54, 89, 201, 201, 201, 201, 201, 18, 18, 18, 18, 14, 14, 12, 12, 5, 1, 2, 2, 2, 1, 1, 23, 23, 23, 54, 54, 201] 201 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 42, 43, 44, 45, 46, 47]) total number of confs: 485 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242095 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242095 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242095/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242095 Building REAL300025242096 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242096' /scratch/stefan/7787021/working/building/REAL300025242096 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242096 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242096/0 /scratch/stefan/7787021/working/building/REAL300025242096 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/991 `/scratch/stefan/7787021/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC(C)(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242096.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242096 none CC(CCNC(=O)CCC(C)(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [61, 60, 61, 70, 83, 84, 84, 84, 176, 190, 201, 201, 201, 52, 60, 23, 51, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 70, 70, 83, 83, 84, 176, 176, 201, 201, 201, 201, 201, 60, 60, 60, 23, 23, 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: 926 number of broken/clashed sets: 130 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242096 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242096 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242096/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242096 Building REAL300025242097 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242097' /scratch/stefan/7787021/working/building/REAL300025242097 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242097 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242097/0 /scratch/stefan/7787021/working/building/REAL300025242097 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/992 `/scratch/stefan/7787021/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)COC1CCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242097.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242097 none CC(CCNC(=O)COC1CCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 64, 75, 89, 102, 108, 108, 108, 191, 201, 201, 201, 201, 201, 201, 43, 64, 23, 42, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 89, 89, 102, 102, 108, 193, 193, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 64, 64, 64, 23, 23, 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: 864 number of broken/clashed sets: 114 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242097 none CC(CCNC(=O)COC1CCCCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 18, 14, 9, 9, 7, 9, 3, 1, 1, 1, 1, 1, 1, 1, 23, 27, 27, 34, 34, 69, 108, 201, 201, 201, 201, 201, 23, 23, 23, 23, 18, 18, 14, 14, 9, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 69, 69, 201] 201 rigid atoms, others: [45, 43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 46, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 49, 50, 51, 52, 53, 54]) total number of confs: 549 number of broken/clashed sets: 114 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242097 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242097 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242097/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242097 Building REAL300025242098 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242098' /scratch/stefan/7787021/working/building/REAL300025242098 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242098 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242098/0 /scratch/stefan/7787021/working/building/REAL300025242098 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/993 `/scratch/stefan/7787021/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1=CC=NC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242098.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242098 none CC(CCNC(=O)CCC1=CC=NC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 80, 87, 88, 88, 88, 201, 201, 201, 201, 201, 201, 201, 63, 77, 27, 62, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 80, 80, 87, 87, 88, 201, 201, 201, 201, 201, 201, 201, 201, 77, 77, 77, 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: 834 number of broken/clashed sets: 101 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242098 none CC(CCNC(=O)CCC1=CC=NC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 22, 18, 12, 12, 4, 12, 2, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 32, 32, 79, 124, 201, 201, 201, 201, 201, 24, 24, 24, 24, 22, 22, 18, 18, 12, 4, 4, 2, 2, 1, 1, 1, 1, 24, 24, 24, 79, 79, 201] 201 rigid atoms, others: [43, 8, 9, 10, 11, 12, 13, 14, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49]) total number of confs: 553 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242098 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242098 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242098/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242098 Building REAL300025242099 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242099' /scratch/stefan/7787021/working/building/REAL300025242099 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242099 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242099/0 /scratch/stefan/7787021/working/building/REAL300025242099 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/994 `/scratch/stefan/7787021/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CCC(=O)NC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242099.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242099 none CC(CCNC(=O)C1CCC(=O)NC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 95, 106, 115, 120, 125, 125, 125, 201, 201, 201, 201, 201, 201, 67, 95, 27, 67, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 106, 115, 115, 120, 120, 125, 201, 201, 201, 201, 201, 201, 201, 201, 95, 95, 95, 27, 27, 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: 713 number of broken/clashed sets: 93 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242099 none CC(CCNC(=O)C1CCC(=O)NC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 21, 24, 24, 32, 32, 69, 109, 201, 201, 201, 201, 201, 21, 21, 21, 21, 17, 17, 16, 16, 8, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 69, 69, 201] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 39, 12, 13, 11, 40, 41, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46, 47, 48]) total number of confs: 526 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242099 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242099 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242099/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242099 Building REAL300025242100 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242100' /scratch/stefan/7787021/working/building/REAL300025242100 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242100 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242100/0 /scratch/stefan/7787021/working/building/REAL300025242100 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/995 `/scratch/stefan/7787021/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=CC=N1) `REAL300025242100.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242100 none COC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 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, 97, 97, 97, 89, 88, 74, 56, 74, 45, 57, 31, 45, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 97, 89, 89, 88, 88, 74, 74, 74, 74, 57, 57, 57, 31, 31, 1, 201, 201] 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]) total number of confs: 589 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242100 none COC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 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, 5, 5, 5, 14, 14, 18, 18, 22, 22, 48, 48, 64, 101, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 14, 18, 18, 18, 18, 22, 22, 22, 64, 64, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 47, 24, 25, 26, 27, 28, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 490 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242100 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242100 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242100/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242100 Building REAL300025242101 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242101' /scratch/stefan/7787021/working/building/REAL300025242101 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242101 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242101/0 /scratch/stefan/7787021/working/building/REAL300025242101 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/996 `/scratch/stefan/7787021/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=NNC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242101.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242101 none CCCC1=NNC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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, 7, 7, 4, 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, 7, 7, 7, 7] 0 hydrogens need 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, 163, 163, 163, 163, 163, 85, 85, 85, 84, 83, 57, 56, 57, 40, 57, 30, 40, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 163, 163, 85, 84, 84, 83, 83, 57, 57, 57, 57, 57, 57, 57, 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: 733 number of broken/clashed sets: 93 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242101 none CCCC1=NNC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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, 7, 7, 4, 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, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 10, 10, 10, 10, 23, 23, 32, 53, 163, 163, 163, 163, 163, 4, 4, 4, 3, 3, 3, 3, 1, 1, 3, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 32, 32, 163] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 34, 35] 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 342 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242101 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242101 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242101/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242101 Building REAL300025242102 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242102' /scratch/stefan/7787021/working/building/REAL300025242102 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242102 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242102/0 /scratch/stefan/7787021/working/building/REAL300025242102 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/997 `/scratch/stefan/7787021/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NNC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242102.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242102 none CCC1=NNC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 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, 7, 4, 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, 7, 7] 0 hydrogens need 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, 151, 151, 125, 125, 125, 124, 116, 109, 104, 109, 84, 104, 30, 83, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 151, 151, 125, 124, 124, 116, 116, 109, 109, 109, 109, 104, 104, 104, 30, 30, 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: 796 number of broken/clashed sets: 122 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242102 none CCC1=NNC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 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, 7, 4, 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, 7, 7] 0 hydrogens 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, 4, 4, 4, 9, 9, 13, 13, 13, 13, 17, 17, 46, 75, 151, 151, 151, 151, 151, 3, 3, 3, 3, 3, 1, 1, 4, 9, 9, 10, 10, 13, 13, 13, 13, 13, 13, 13, 46, 46, 151] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 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, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 371 number of broken/clashed sets: 122 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242102 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242102 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242102/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242102 Building REAL300025242103 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242103' /scratch/stefan/7787021/working/building/REAL300025242103 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242103 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242103/0 /scratch/stefan/7787021/working/building/REAL300025242103 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/998 `/scratch/stefan/7787021/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NNC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242103.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242103 none CC(C)C1=NNC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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, 7, 7, 4, 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, 7, 7, 7, 7] 0 hydrogens need 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, 141, 141, 141, 138, 134, 128, 113, 128, 81, 113, 33, 80, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 141, 138, 138, 134, 134, 128, 128, 128, 128, 113, 113, 113, 33, 33, 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: 639 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: REAL300025242103 none CC(C)C1=NNC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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, 7, 7, 4, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 1, 4, 4, 4, 12, 14, 20, 20, 25, 25, 29, 29, 57, 99, 201, 201, 201, 201, 201, 2, 2, 2, 1, 2, 2, 2, 1, 1, 4, 12, 12, 15, 15, 20, 20, 20, 20, 25, 25, 25, 57, 57, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 35, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 498 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242103 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242103 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242103/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242103 Building REAL300025242104 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242104' /scratch/stefan/7787021/working/building/REAL300025242104 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025242104 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242104/0 /scratch/stefan/7787021/working/building/REAL300025242104 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/999 `/scratch/stefan/7787021/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=NNC2=C1CCC2)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242104.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242104 none CC(CCNC(=O)C1=NNC2=C1CCC2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 8, 8, 1, 1, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 113, 130, 164, 181, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 68, 113, 30, 67, 13, 1, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 164, 164, 181, 181, 201, 201, 201, 201, 201, 201, 201, 201, 113, 113, 113, 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: 823 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242104 none CC(CCNC(=O)C1=NNC2=C1CCC2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 8, 8, 1, 1, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 22, 22, 35, 35, 68, 107, 201, 201, 201, 201, 201, 13, 13, 13, 13, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 68, 68, 201] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 40, 3, 41, 36, 38, 42, 39, 37] set([0, 1, 2, 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]) total number of confs: 518 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242104 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025242104/1 /scratch/stefan/7787021/working/building/REAL300025242104 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1000 `/scratch/stefan/7787021/working/3D/1000' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=C2CCCC2=NN1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242104.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025242104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242104/1/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: REAL300025242104 none CC(CCNC(=O)C1=C2CCCC2=NN1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [141, 119, 141, 169, 183, 190, 190, 190, 201, 201, 201, 201, 201, 201, 201, 90, 119, 32, 90, 13, 1, 1, 1, 1, 1, 1, 1, 141, 141, 141, 141, 169, 169, 183, 183, 190, 201, 201, 201, 201, 201, 201, 201, 119, 119, 119, 32, 32, 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: 777 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: REAL300025242104 none CC(CCNC(=O)C1=C2CCCC2=NN1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 14, 19, 19, 30, 30, 72, 107, 201, 201, 201, 201, 201, 14, 14, 14, 14, 11, 11, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 72, 72, 201] 201 rigid atoms, others: [36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47, 48]) total number of confs: 525 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242104 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242104 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242104/0.* 1: /scratch/stefan/7787021/working/building/REAL300025242104/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242104 Building REAL300025242105 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242105' /scratch/stefan/7787021/working/building/REAL300025242105 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025242105 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242105/0 /scratch/stefan/7787021/working/building/REAL300025242105 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1001 `/scratch/stefan/7787021/working/3D/1001' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=NNN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242105.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242105 none CC(CCNC(=O)C1=NNN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 1, 8, 8, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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: [123, 105, 123, 160, 179, 201, 201, 201, 201, 201, 201, 201, 62, 105, 26, 61, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 160, 160, 179, 179, 201, 201, 201, 105, 105, 105, 26, 26, 1] 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]) total number of confs: 824 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: REAL300025242105 none CC(CCNC(=O)C1=NNN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 1, 8, 8, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 15, 23, 23, 36, 36, 65, 104, 201, 201, 201, 201, 201, 15, 15, 15, 15, 8, 8, 6, 6, 2, 1, 1, 23, 23, 23, 65, 65, 201] 201 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 509 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242105 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025242105/1 /scratch/stefan/7787021/working/building/REAL300025242105 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1002 `/scratch/stefan/7787021/working/3D/1002' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CN=NN1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242105.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025242105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242105/1/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: REAL300025242105 none CC(CCNC(=O)C1=CN=NN1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 1, 1, 8, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 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, 103, 123, 154, 158, 201, 201, 201, 201, 201, 201, 201, 70, 103, 29, 70, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 154, 154, 158, 158, 201, 201, 201, 103, 103, 103, 29, 29, 1] 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]) total number of confs: 802 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242105 none CC(CCNC(=O)C1=CN=NN1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 1, 11, 1, 1, 8, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 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, 8, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 13, 24, 24, 37, 37, 69, 106, 201, 201, 201, 201, 201, 13, 13, 13, 13, 8, 8, 7, 7, 2, 1, 1, 24, 24, 24, 69, 69, 201] 201 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 507 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242105 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242105 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242105/0.* 1: /scratch/stefan/7787021/working/building/REAL300025242105/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242105 Building REAL300025242106 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242106' /scratch/stefan/7787021/working/building/REAL300025242106 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242106 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242106/0 /scratch/stefan/7787021/working/building/REAL300025242106 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1003 `/scratch/stefan/7787021/working/3D/1003' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CN1CCCCC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242106.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242106 none CC(CCNC(=O)CN1CCCCC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 73, 76, 100, 129, 134, 134, 134, 195, 201, 201, 201, 201, 201, 201, 67, 73, 28, 66, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 100, 100, 129, 129, 134, 195, 195, 201, 201, 201, 201, 201, 201, 201, 201, 73, 73, 73, 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: 848 number of broken/clashed sets: 117 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242106 none CC(CCNC(=O)CN1CCCCC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 20, 12, 12, 4, 12, 1, 1, 1, 1, 1, 1, 1, 1, 29, 31, 31, 36, 36, 66, 103, 201, 201, 201, 201, 201, 29, 29, 29, 29, 24, 24, 20, 20, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 66, 66, 201] 201 rigid atoms, others: [45, 11, 38, 7, 8, 9, 10, 39, 12, 13, 14, 44, 40, 43, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 46, 47, 48, 49, 50, 51]) total number of confs: 529 number of broken/clashed sets: 117 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242106 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242106 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242106/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242106 Building REAL300025242107 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242107' /scratch/stefan/7787021/working/building/REAL300025242107 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242107 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242107/0 /scratch/stefan/7787021/working/building/REAL300025242107 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1004) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1004 `/scratch/stefan/7787021/working/3D/1004' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CN(C)C(=O)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242107.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242107 none CC(CCNC(=O)C1=CN(C)C(=O)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 11, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 62, 70, 71, 72, 72, 72, 72, 201, 201, 201, 201, 201, 201, 201, 52, 62, 24, 52, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 71, 71, 72, 72, 72, 201, 201, 201, 201, 201, 201, 62, 62, 62, 24, 24, 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: 447 number of broken/clashed sets: 84 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242107 none CC(CCNC(=O)C1=CN(C)C(=O)C=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 11, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 9, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 18, 18, 22, 22, 48, 86, 201, 201, 201, 201, 201, 14, 14, 14, 14, 11, 11, 11, 11, 5, 1, 2, 2, 2, 1, 1, 18, 18, 18, 48, 48, 201] 201 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 42, 43, 44, 45, 46, 47]) total number of confs: 457 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242107 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242107 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242107/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242107 Building REAL300025242108 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242108' /scratch/stefan/7787021/working/building/REAL300025242108 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242108 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242108/0 /scratch/stefan/7787021/working/building/REAL300025242108 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1005) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1005 `/scratch/stefan/7787021/working/3D/1005' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=NN1C) `REAL300025242108.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242108 none CCC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=NN1C 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 115, 115, 81, 81, 81, 81, 73, 70, 70, 70, 54, 70, 19, 53, 10, 1, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 201, 201, 201, 201, 201, 81, 81, 81, 73, 73, 70, 70, 70, 70, 70, 70, 70, 19, 19, 1, 115, 115, 115, 115] 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: 869 number of broken/clashed sets: 107 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242108 none CCC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=NN1C 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 7, 10, 14, 14, 14, 14, 19, 19, 43, 68, 115, 115, 115, 115, 115, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 7, 7, 10, 10, 14, 14, 14, 14, 14, 14, 14, 43, 43, 115, 1, 2, 2, 2] 201 rigid atoms, others: [1, 2, 3, 4, 47, 23, 24, 25, 26] set([0, 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, 48, 49, 50]) total number of confs: 328 number of broken/clashed sets: 107 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242108 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242108 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242108/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242108 Building REAL300025242109 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242109' /scratch/stefan/7787021/working/building/REAL300025242109 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242109 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242109/0 /scratch/stefan/7787021/working/building/REAL300025242109 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1006) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1006 `/scratch/stefan/7787021/working/3D/1006' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CN1CCCNC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242109.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242109 none CC(CCNC(=O)CN1CCCNC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 8, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 87, 93, 116, 143, 168, 168, 168, 201, 201, 201, 201, 201, 201, 201, 79, 87, 31, 79, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 116, 116, 143, 143, 168, 201, 201, 201, 201, 201, 201, 201, 201, 201, 87, 87, 87, 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: 852 number of broken/clashed sets: 121 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242109 none CC(CCNC(=O)CN1CCCNC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 8, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 20, 10, 10, 2, 10, 1, 1, 1, 1, 1, 1, 1, 1, 26, 28, 28, 33, 33, 64, 101, 201, 201, 201, 201, 201, 26, 26, 26, 26, 23, 23, 20, 20, 10, 2, 2, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 64, 64, 201] 201 rigid atoms, others: [11, 38, 7, 8, 9, 10, 39, 12, 13, 14, 44, 40, 43, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 48, 49, 50]) total number of confs: 513 number of broken/clashed sets: 121 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242109 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242109 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242109/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242109 Building REAL300025242110 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242110' /scratch/stefan/7787021/working/building/REAL300025242110 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242110 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242110/0 /scratch/stefan/7787021/working/building/REAL300025242110 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1007) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1007 `/scratch/stefan/7787021/working/3D/1007' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1(C)C(C)(C)C1(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242110.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242110 none CC(CCNC(=O)C1(C)C(C)(C)C1(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 103, 128, 148, 160, 168, 168, 168, 201, 201, 201, 201, 201, 201, 201, 66, 103, 29, 65, 13, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 128, 148, 148, 160, 160, 168, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 103, 103, 29, 29, 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: 800 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: REAL300025242110 none CC(CCNC(=O)C1(C)C(C)(C)C1(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 15, 23, 23, 35, 35, 65, 103, 201, 201, 201, 201, 201, 15, 15, 15, 15, 11, 11, 9, 9, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 23, 23, 23, 65, 65, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 533 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242110 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242110 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242110/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242110 Building REAL300025242111 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242111' /scratch/stefan/7787021/working/building/REAL300025242111 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242111 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242111/0 /scratch/stefan/7787021/working/building/REAL300025242111 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1008) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1008 `/scratch/stefan/7787021/working/3D/1008' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CCCC1) `REAL300025242111.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242111 none C=CCC1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CCCC1 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.3', 'C.2', '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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 138, 138, 138, 127, 119, 102, 98, 102, 74, 98, 30, 74, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 138, 127, 127, 119, 119, 102, 102, 102, 102, 98, 98, 98, 30, 30, 1, 201, 201, 201, 201, 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: 778 number of broken/clashed sets: 118 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242111 none C=CCC1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CCCC1 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.3', 'C.2', '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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 3, 3, 3, 7, 9, 14, 14, 15, 15, 20, 20, 44, 78, 201, 201, 201, 201, 201, 1, 1, 1, 1, 6, 6, 6, 4, 4, 3, 7, 7, 9, 9, 14, 14, 14, 14, 15, 15, 15, 44, 44, 201, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 47, 48, 49, 50, 51, 52, 53, 54, 23, 24, 25, 26] set([0, 1, 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: 457 number of broken/clashed sets: 118 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242111 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242111 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242111/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242111 Building REAL300025242112 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242112' /scratch/stefan/7787021/working/building/REAL300025242112 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242112 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242112/0 /scratch/stefan/7787021/working/building/REAL300025242112 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1009) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1009 `/scratch/stefan/7787021/working/3D/1009' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)NC=N1) `REAL300025242112.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242112 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 117, 117, 117, 116, 111, 103, 87, 103, 65, 87, 27, 65, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 117, 116, 116, 111, 111, 103, 103, 103, 103, 87, 87, 87, 27, 27, 1, 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]) total number of confs: 583 number of broken/clashed sets: 104 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242112 none CC1=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 16, 22, 22, 26, 26, 31, 31, 67, 111, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 8, 14, 14, 17, 17, 22, 22, 22, 22, 26, 26, 26, 67, 67, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 43, 44, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 546 number of broken/clashed sets: 104 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242112 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242112 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242112/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242112 Building REAL300025242113 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242113' /scratch/stefan/7787021/working/building/REAL300025242113 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242113 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242113/0 /scratch/stefan/7787021/working/building/REAL300025242113 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1010) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1010 `/scratch/stefan/7787021/working/3D/1010' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CC12CCOCC2)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242113.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242113 none CC(CCNC(=O)C1CC12CCOCC2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 81, 100, 110, 115, 122, 122, 122, 201, 201, 201, 201, 201, 201, 201, 56, 81, 26, 56, 13, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 110, 110, 115, 115, 122, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 81, 81, 81, 26, 26, 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: 84 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242113 none CC(CCNC(=O)C1CC12CCOCC2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7] 0 hydrogens 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, 11, 10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 22, 22, 29, 29, 58, 95, 201, 201, 201, 201, 201, 17, 17, 17, 17, 11, 11, 10, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 58, 58, 201] 201 rigid atoms, others: [45, 43, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 44, 40, 46, 41, 39, 42, 5] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 47, 48, 49, 50, 51, 52]) total number of confs: 482 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242113 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242113 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242113/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242113 Building REAL300025242114 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242114' /scratch/stefan/7787021/working/building/REAL300025242114 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242114 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242114/0 /scratch/stefan/7787021/working/building/REAL300025242114 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1011) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1011 `/scratch/stefan/7787021/working/3D/1011' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C(C)C1CCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242114.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242114 none CC(CCNC(=O)C(C)C1CCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 54, 60, 78, 86, 96, 96, 96, 198, 198, 201, 201, 201, 201, 201, 45, 54, 22, 44, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 78, 78, 86, 86, 96, 198, 198, 198, 198, 201, 201, 201, 201, 201, 201, 201, 201, 201, 54, 54, 54, 22, 22, 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: 863 number of broken/clashed sets: 106 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242114 none CC(CCNC(=O)C(C)C1CCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 17, 16, 9, 9, 4, 9, 1, 4, 1, 1, 1, 1, 1, 1, 24, 24, 24, 30, 30, 59, 96, 201, 201, 201, 201, 201, 24, 24, 24, 24, 19, 19, 16, 16, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 59, 59, 201] 201 rigid atoms, others: [45, 43, 7, 40, 9, 10, 11, 12, 13, 14, 44, 48, 46, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 512 number of broken/clashed sets: 106 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242114 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242114 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242114/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242114 Building REAL300025242115 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242115' /scratch/stefan/7787021/working/building/REAL300025242115 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242115 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242115/0 /scratch/stefan/7787021/working/building/REAL300025242115 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1012) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1012 `/scratch/stefan/7787021/working/3D/1012' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1CC(=O)NC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242115.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242115 none CC(CCNC(=O)CC1CC(=O)NC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [69, 69, 69, 72, 83, 84, 84, 84, 180, 201, 201, 201, 201, 201, 201, 62, 69, 30, 62, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 72, 72, 83, 83, 84, 180, 180, 201, 201, 201, 201, 69, 69, 69, 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: 781 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242115 none CC(CCNC(=O)CC1CC(=O)NC1=O)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [30, 29, 25, 19, 19, 6, 19, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 31, 31, 64, 105, 201, 201, 201, 201, 201, 30, 30, 30, 30, 29, 29, 25, 25, 19, 6, 6, 1, 1, 1, 1, 30, 30, 30, 64, 64, 201] 201 rigid atoms, others: [11, 38, 7, 8, 9, 10, 39, 12, 13, 14, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47]) total number of confs: 514 number of broken/clashed sets: 136 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242115 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242115 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242115/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242115 Building REAL300025242116 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242116' /scratch/stefan/7787021/working/building/REAL300025242116 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242116 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242116/0 /scratch/stefan/7787021/working/building/REAL300025242116 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1013) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1013 `/scratch/stefan/7787021/working/3D/1013' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1(C)CC2CCC1C2)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242116.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242116 none CC(CCNC(=O)C1(C)CC2CCC1C2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [143, 124, 143, 174, 192, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 78, 124, 30, 78, 13, 1, 1, 1, 1, 1, 1, 1, 143, 143, 143, 143, 174, 174, 192, 192, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 124, 124, 124, 30, 30, 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: 797 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: REAL300025242116 none CC(CCNC(=O)C1(C)CC2CCC1C2)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [14, 9, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 14, 22, 22, 39, 39, 67, 107, 201, 201, 201, 201, 201, 14, 14, 14, 14, 10, 10, 8, 8, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 67, 67, 201] 201 rigid atoms, others: [45, 11, 5, 7, 8, 9, 10, 39, 12, 13, 14, 44, 48, 40, 46, 43, 41, 47, 42] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 49, 50, 51, 52, 53, 54]) total number of confs: 511 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242116 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242116 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242116/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242116 Building REAL300025242117 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242117' /scratch/stefan/7787021/working/building/REAL300025242117 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242117 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242117/0 /scratch/stefan/7787021/working/building/REAL300025242117 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1014) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1014 `/scratch/stefan/7787021/working/3D/1014' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C(C)O1) `REAL300025242117.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242117 none CCC1=NC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C(C)O1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 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, 138, 138, 138, 138, 138, 138, 93, 93, 65, 57, 65, 43, 58, 29, 43, 12, 1, 1, 1, 1, 1, 1, 1, 138, 138, 138, 201, 201, 201, 201, 201, 138, 93, 93, 93, 93, 65, 65, 65, 65, 58, 58, 58, 29, 29, 1, 138, 138, 138] 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]) total number of confs: 932 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242117 none CCC1=NC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C(C)O1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 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: [8, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 11, 11, 21, 21, 30, 49, 138, 138, 138, 138, 138, 1, 1, 1, 8, 8, 8, 7, 7, 2, 5, 5, 6, 6, 9, 9, 9, 9, 11, 11, 11, 30, 30, 138, 2, 2, 2] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 26] set([0, 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: 326 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242117 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242117 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242117/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242117 Building REAL300025242118 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242118' /scratch/stefan/7787021/working/building/REAL300025242118 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242118 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242118/0 /scratch/stefan/7787021/working/building/REAL300025242118 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1015) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1015 `/scratch/stefan/7787021/working/3D/1015' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C(C)C(C)C(C)(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242118.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242118 none CC(CCNC(=O)C(C)C(C)C(C)(C)C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 101, 121, 140, 157, 189, 189, 189, 201, 201, 201, 201, 201, 201, 201, 68, 101, 28, 68, 13, 1, 1, 1, 1, 1, 1, 1, 121, 121, 121, 121, 140, 140, 157, 157, 189, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 101, 101, 28, 28, 1] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26, 58] 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, 56, 57]) total number of confs: 820 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242118 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242118 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242118/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242118 Building REAL300025242119 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242119' /scratch/stefan/7787021/working/building/REAL300025242119 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242119 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242119/0 /scratch/stefan/7787021/working/building/REAL300025242119 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1016) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1016 `/scratch/stefan/7787021/working/3D/1016' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=CO1)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242119.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242119 none CC(CC1=CC=CO1)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens 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, 88, 159, 175, 201, 201, 201, 201, 88, 88, 88, 88, 56, 55, 56, 39, 56, 27, 39, 12, 1, 1, 1, 1, 1, 1, 1, 159, 159, 159, 159, 175, 175, 201, 201, 201, 88, 88, 88, 88, 88, 56, 56, 56, 56, 56, 56, 56, 27, 27, 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: 889 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: REAL300025242119 none CC(CC1=CC=CO1)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 10, 18, 18, 18, 23, 23, 24, 24, 24, 24, 55, 55, 73, 107, 201, 201, 201, 201, 201, 10, 10, 10, 10, 3, 3, 1, 1, 1, 18, 23, 23, 23, 23, 24, 24, 24, 24, 24, 24, 24, 73, 73, 201] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 35] 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, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 533 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242119 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242119 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242119/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242119 Building REAL300025242120 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242120' /scratch/stefan/7787021/working/building/REAL300025242120 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242120 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242120/0 /scratch/stefan/7787021/working/building/REAL300025242120 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1017) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1017 `/scratch/stefan/7787021/working/3D/1017' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CC1CCC(=O)N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242120.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242120 none CC(CCNC(=O)CC1CCC(=O)N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 81, 87, 87, 87, 87, 188, 201, 201, 201, 201, 201, 67, 79, 28, 67, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 81, 81, 87, 87, 87, 188, 188, 201, 201, 201, 201, 201, 201, 79, 79, 79, 28, 28, 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: 809 number of broken/clashed sets: 97 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242120 none CC(CCNC(=O)CC1CCC(=O)N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 18, 18, 5, 18, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 33, 33, 71, 119, 201, 201, 201, 201, 201, 24, 24, 24, 24, 23, 23, 21, 21, 18, 5, 5, 1, 1, 1, 1, 1, 1, 24, 24, 24, 71, 71, 201] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 40, 41, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 522 number of broken/clashed sets: 97 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242120 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242120 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242120/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242120 Building REAL300025242121 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242121' /scratch/stefan/7787021/working/building/REAL300025242121 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242121 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242121/0 /scratch/stefan/7787021/working/building/REAL300025242121 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1018) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1018 `/scratch/stefan/7787021/working/3D/1018' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CC1) `REAL300025242121.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242121 none CNC(=O)C1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 118, 118, 118, 111, 93, 77, 64, 77, 42, 64, 23, 41, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 118, 111, 111, 93, 93, 77, 77, 77, 77, 64, 64, 64, 23, 23, 1, 201, 201, 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]) total number of confs: 796 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: REAL300025242121 none CNC(=O)C1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 5, 5, 5, 11, 15, 20, 20, 27, 27, 37, 37, 69, 107, 201, 201, 201, 201, 201, 1, 1, 5, 5, 5, 5, 5, 11, 11, 15, 15, 20, 20, 20, 20, 27, 27, 27, 69, 69, 201, 1, 1, 1, 1] 201 rigid atoms, others: [2, 4, 5, 45, 46, 47, 48, 24, 25] set([0, 1, 3, 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]) total number of confs: 544 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242121 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242121 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242121/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242121 Building REAL300025242122 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242122' /scratch/stefan/7787021/working/building/REAL300025242122 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242122 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242122/0 /scratch/stefan/7787021/working/building/REAL300025242122 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1019) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1019 `/scratch/stefan/7787021/working/3D/1019' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=C1F) `REAL300025242122.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242122 none CC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=C1F 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 84, 84, 84, 80, 79, 66, 51, 66, 42, 52, 29, 42, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 84, 80, 80, 79, 79, 66, 66, 66, 66, 52, 52, 52, 29, 29, 1, 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]) total number of confs: 539 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: REAL300025242122 none CC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=C1F 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations 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, 5, 13, 13, 16, 16, 21, 21, 45, 45, 62, 97, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 5, 13, 13, 13, 13, 16, 16, 16, 16, 21, 21, 21, 62, 62, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 494 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242122 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242122 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242122/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242122 Building REAL300025242123 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242123' /scratch/stefan/7787021/working/building/REAL300025242123 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242123 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242123/0 /scratch/stefan/7787021/working/building/REAL300025242123 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1020) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1020 `/scratch/stefan/7787021/working/3D/1020' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C(C)O1) `REAL300025242123.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242123 none CC1=C(C)C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C(C)O1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 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, 201, 201, 88, 88, 88, 86, 81, 80, 75, 80, 60, 75, 23, 60, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 88, 86, 86, 81, 81, 80, 80, 80, 80, 75, 75, 75, 23, 23, 1, 201, 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]) total number of confs: 466 number of broken/clashed sets: 114 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242123 none CC1=C(C)C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C(C)O1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 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, 1, 1, 10, 10, 10, 15, 19, 24, 24, 26, 26, 31, 31, 63, 110, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 2, 2, 2, 10, 15, 15, 19, 19, 24, 24, 24, 24, 26, 26, 26, 63, 63, 201, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 48, 49, 50, 24, 25, 26] set([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: 524 number of broken/clashed sets: 114 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242123 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242123 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242123/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242123 Building REAL300025242124 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242124' /scratch/stefan/7787021/working/building/REAL300025242124 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242124 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242124/0 /scratch/stefan/7787021/working/building/REAL300025242124 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1021) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1021 `/scratch/stefan/7787021/working/3D/1021' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=N1) `REAL300025242124.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242124 none COC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 181, 181, 181, 166, 159, 129, 86, 129, 67, 86, 42, 67, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 181, 166, 166, 159, 159, 129, 129, 129, 129, 86, 86, 86, 42, 42, 1, 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]) total number of confs: 856 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: REAL300025242124 none COC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 15, 17, 22, 22, 26, 26, 50, 50, 69, 106, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 5, 15, 15, 18, 18, 22, 22, 22, 22, 26, 26, 26, 69, 69, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 47, 25, 26, 30, 31] set([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: 532 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242124 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242124 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242124/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242124 Building REAL300025242125 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242125' /scratch/stefan/7787021/working/building/REAL300025242125 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242125 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242125/0 /scratch/stefan/7787021/working/building/REAL300025242125 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1022) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1022 `/scratch/stefan/7787021/working/3D/1022' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C(C)=C1) `REAL300025242125.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242125 none CC1=NN(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C(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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 194, 81, 81, 81, 68, 68, 47, 43, 47, 31, 43, 21, 31, 11, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 194, 194, 81, 68, 68, 68, 68, 47, 47, 47, 47, 43, 43, 43, 21, 21, 1, 201, 201, 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]) total number of confs: 820 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242125 none CC1=NN(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C(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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 10, 10, 10, 18, 18, 22, 22, 23, 23, 46, 46, 64, 101, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 4, 4, 10, 18, 18, 18, 18, 22, 22, 22, 22, 23, 23, 23, 64, 64, 201, 2, 2, 2, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 50, 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, 45, 46, 47, 48, 49]) total number of confs: 536 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242125 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242125 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242125/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242125 Building REAL300025242126 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242126' /scratch/stefan/7787021/working/building/REAL300025242126 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242126 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242126/0 /scratch/stefan/7787021/working/building/REAL300025242126 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1023) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1023 `/scratch/stefan/7787021/working/3D/1023' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)O1) `REAL300025242126.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242126 none COCC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 116, 116, 116, 116, 116, 116, 116, 103, 103, 63, 62, 63, 50, 63, 32, 50, 13, 1, 1, 1, 1, 1, 1, 1, 116, 201, 201, 201, 201, 201, 116, 116, 116, 103, 103, 103, 103, 63, 63, 63, 63, 63, 63, 63, 32, 32, 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: 918 number of broken/clashed sets: 114 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242126 none COCC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 4, 4, 6, 6, 6, 6, 14, 14, 23, 42, 116, 116, 116, 116, 116, 1, 10, 10, 10, 6, 6, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 23, 23, 116] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 26] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 259 number of broken/clashed sets: 114 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242126 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242126 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242126/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242126 Building REAL300025242127 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242127' /scratch/stefan/7787021/working/building/REAL300025242127 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242127 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242127/0 /scratch/stefan/7787021/working/building/REAL300025242127 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1024) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1024 `/scratch/stefan/7787021/working/3D/1024' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1) `REAL300025242127.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242127 none CC1=NN(C)C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 53, 53, 53, 52, 52, 37, 37, 37, 28, 37, 23, 28, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 53, 52, 52, 52, 52, 37, 37, 37, 37, 37, 37, 37, 23, 23, 1, 201] 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, 50]) total number of confs: 777 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: REAL300025242127 none CC1=NN(C)C(CC(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 16, 16, 17, 17, 18, 18, 42, 42, 57, 96, 201, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 3, 3, 10, 16, 16, 16, 16, 17, 17, 17, 17, 18, 18, 18, 57, 57, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 50, 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, 48, 49]) total number of confs: 501 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242127 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242127 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242127/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242127 Building REAL300025242128 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242128' /scratch/stefan/7787021/working/building/REAL300025242128 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242128 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242128/0 /scratch/stefan/7787021/working/building/REAL300025242128 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1025) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1025 `/scratch/stefan/7787021/working/3D/1025' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)CC1) `REAL300025242128.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242128 none COCC1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 78, 78, 78, 75, 61, 50, 50, 50, 41, 50, 20, 41, 13, 1, 1, 1, 1, 1, 1, 1, 182, 182, 201, 201, 201, 201, 201, 78, 75, 75, 61, 61, 50, 50, 50, 50, 50, 50, 50, 20, 20, 1, 182, 182, 182, 182] 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: 734 number of broken/clashed sets: 140 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242128 none COCC1(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 6, 6, 6, 10, 13, 15, 15, 17, 17, 21, 21, 49, 82, 182, 182, 182, 182, 182, 1, 1, 8, 8, 8, 5, 5, 6, 10, 10, 13, 13, 15, 15, 15, 15, 17, 17, 17, 49, 49, 182, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 45, 46, 47, 48, 23, 24] set([0, 1, 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: 462 number of broken/clashed sets: 140 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242128 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242128 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242128/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242128 Building REAL300025242129 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242129' /scratch/stefan/7787021/working/building/REAL300025242129 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242129 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242129/0 /scratch/stefan/7787021/working/building/REAL300025242129 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1026) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1026 `/scratch/stefan/7787021/working/3D/1026' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242129.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242129 none COCC(C)(C)C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 115, 190, 190, 115, 115, 114, 103, 83, 73, 83, 50, 73, 24, 49, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 190, 190, 190, 190, 190, 190, 115, 114, 114, 103, 103, 83, 83, 83, 83, 73, 73, 73, 24, 24, 1] 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]) total number of confs: 908 number of broken/clashed sets: 113 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242129 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242129 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242129/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242129 Building REAL300025242130 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242130' /scratch/stefan/7787021/working/building/REAL300025242130 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242130 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242130/0 /scratch/stefan/7787021/working/building/REAL300025242130 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1027) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1027 `/scratch/stefan/7787021/working/3D/1027' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1=NOC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242130.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242130 none CC(CCNC(=O)CCC1=NOC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 12, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 42, 51, 64, 70, 70, 70, 163, 183, 201, 201, 201, 201, 39, 42, 22, 38, 13, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 51, 51, 64, 64, 70, 163, 163, 183, 183, 201, 201, 42, 42, 42, 22, 22, 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: 821 number of broken/clashed sets: 143 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242130 none CC(CCNC(=O)CCC1=NOC=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 12, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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] 0 hydrogens 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, 34, 29, 21, 21, 8, 21, 4, 1, 1, 1, 1, 1, 1, 37, 38, 38, 40, 40, 81, 117, 201, 201, 201, 201, 201, 37, 37, 37, 37, 34, 34, 29, 29, 21, 8, 8, 4, 4, 1, 1, 38, 38, 38, 81, 81, 201] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 584 number of broken/clashed sets: 143 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242130 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242130 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242130/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242130 Building REAL300025242131 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242131' /scratch/stefan/7787021/working/building/REAL300025242131 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242131 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242131/0 /scratch/stefan/7787021/working/building/REAL300025242131 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1028) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1028 `/scratch/stefan/7787021/working/3D/1028' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC1=CN=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242131.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242131 none CC(CCNC(=O)CCC1=CN=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 87, 92, 99, 105, 107, 107, 107, 200, 201, 201, 201, 201, 201, 201, 65, 87, 27, 64, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 99, 99, 105, 105, 107, 200, 200, 201, 201, 201, 201, 201, 87, 87, 87, 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: 843 number of broken/clashed sets: 117 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242131 none CC(CCNC(=O)CCC1=CN=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 28, 18, 18, 5, 18, 3, 1, 1, 1, 1, 1, 1, 1, 32, 34, 34, 36, 36, 71, 115, 201, 201, 201, 201, 201, 32, 32, 32, 32, 29, 29, 28, 28, 18, 5, 5, 3, 3, 1, 1, 1, 34, 34, 34, 71, 71, 201] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48]) total number of confs: 546 number of broken/clashed sets: 134 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242131 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242131 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242131/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242131 Building REAL300025242132 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242132' /scratch/stefan/7787021/working/building/REAL300025242132 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242132 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242132/0 /scratch/stefan/7787021/working/building/REAL300025242132 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1029) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1029 `/scratch/stefan/7787021/working/3D/1029' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CN=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1) `REAL300025242132.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242132 none CCC1=CN=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 117, 117, 117, 117, 117, 45, 45, 45, 45, 44, 35, 34, 35, 25, 35, 18, 25, 11, 1, 1, 1, 1, 1, 1, 1, 117, 201, 201, 201, 201, 201, 117, 117, 45, 45, 45, 44, 44, 35, 35, 35, 35, 35, 35, 35, 18, 18, 1, 117] 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, 49]) total number of confs: 792 number of broken/clashed sets: 74 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242132 none CCC1=CN=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens 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, 1, 5, 5, 5, 11, 11, 11, 11, 11, 11, 23, 23, 29, 49, 117, 117, 117, 117, 117, 1, 2, 2, 2, 2, 2, 1, 1, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 29, 29, 117, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 49, 26] set([0, 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: 264 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242132 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242132 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242132/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242132 Building REAL300025242133 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242133' /scratch/stefan/7787021/working/building/REAL300025242133 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242133 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242133/0 /scratch/stefan/7787021/working/building/REAL300025242133 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1030) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1030 `/scratch/stefan/7787021/working/3D/1030' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1CC(=O)NC(=O)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242133.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242133 none CC(CCNC(=O)C1CC(=O)NC(=O)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 1, 11, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [82, 82, 82, 85, 89, 91, 91, 91, 201, 201, 201, 201, 201, 201, 201, 63, 82, 24, 63, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 85, 85, 89, 89, 91, 201, 201, 201, 201, 201, 201, 82, 82, 82, 24, 24, 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: 655 number of broken/clashed sets: 101 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242133 none CC(CCNC(=O)C1CC(=O)NC(=O)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 1, 11, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [23, 19, 16, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 29, 29, 72, 118, 201, 201, 201, 201, 201, 23, 23, 23, 23, 19, 19, 16, 16, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 72, 72, 201] 201 rigid atoms, others: [36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47]) total number of confs: 530 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242133 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242133 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242133/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242133 Building REAL300025242134 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242134' /scratch/stefan/7787021/working/building/REAL300025242134 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242134 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242134/0 /scratch/stefan/7787021/working/building/REAL300025242134 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1031) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1031 `/scratch/stefan/7787021/working/3D/1031' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=NN(C)N=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242134.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242134 none CC(CCNC(=O)C1=NN(C)N=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 8, 8, 5, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [120, 102, 120, 158, 178, 201, 201, 201, 201, 201, 201, 201, 201, 62, 102, 26, 62, 13, 1, 1, 1, 1, 1, 1, 1, 120, 120, 120, 120, 158, 158, 178, 178, 201, 201, 201, 201, 201, 102, 102, 102, 26, 26, 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: 828 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242134 none CC(CCNC(=O)C1=NN(C)N=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 8, 1, 11, 1, 8, 8, 5, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [14, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 21, 21, 34, 34, 64, 103, 201, 201, 201, 201, 201, 14, 14, 14, 14, 8, 8, 6, 6, 2, 2, 2, 2, 1, 21, 21, 21, 64, 64, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 515 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242134 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242134 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242134/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242134 Building REAL300025242135 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242135' /scratch/stefan/7787021/working/building/REAL300025242135 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242135 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242135/0 /scratch/stefan/7787021/working/building/REAL300025242135 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1032) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1032 `/scratch/stefan/7787021/working/3D/1032' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CN=CC(Cl)=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242135.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242135 none CC(CCNC(=O)C1=CN=CC(Cl)=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 8, 1, 1, 16, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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] 0 hydrogens 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, 58, 67, 70, 74, 74, 74, 74, 201, 201, 201, 201, 201, 201, 48, 58, 24, 47, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 70, 70, 74, 74, 74, 201, 201, 201, 58, 58, 58, 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: 469 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242135 none CC(CCNC(=O)C1=CN=CC(Cl)=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 8, 1, 1, 16, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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] 0 hydrogens 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, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 16, 20, 20, 24, 24, 52, 91, 201, 201, 201, 201, 201, 16, 16, 16, 16, 12, 12, 10, 10, 5, 1, 1, 1, 20, 20, 20, 52, 52, 201] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 470 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242135 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242135 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242135/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242135 Building REAL300025242136 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242136' /scratch/stefan/7787021/working/building/REAL300025242136 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242136 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242136/0 /scratch/stefan/7787021/working/building/REAL300025242136 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1033) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1033 `/scratch/stefan/7787021/working/3D/1033' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=CS1) `REAL300025242136.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242136 none CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 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, 7, 7] 0 hydrogens need 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, 121, 121, 121, 121, 115, 111, 96, 111, 69, 96, 30, 69, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 121, 121, 121, 115, 115, 111, 111, 111, 111, 96, 96, 96, 30, 30, 1, 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]) total number of confs: 606 number of broken/clashed sets: 84 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242136 none CC1=CC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 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, 7, 7] 0 hydrogens need rotated 201 conformations 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, 12, 17, 17, 22, 22, 26, 26, 50, 92, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 5, 10, 10, 13, 13, 17, 17, 17, 17, 22, 22, 22, 50, 50, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 44, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 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: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242136 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242136 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242136/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242136 Building REAL300025242137 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242137' /scratch/stefan/7787021/working/building/REAL300025242137 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242137 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242137/0 /scratch/stefan/7787021/working/building/REAL300025242137 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1034) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1034 `/scratch/stefan/7787021/working/3D/1034' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)COC1=CC=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242137.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242137 none CC(CCNC(=O)COC1=CC=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 100, 111, 112, 112, 112, 145, 177, 201, 201, 201, 201, 201, 67, 93, 29, 67, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 100, 100, 111, 111, 112, 145, 145, 201, 201, 201, 201, 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: 688 number of broken/clashed sets: 131 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242137 none CC(CCNC(=O)COC1=CC=CN=C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 20, 17, 15, 15, 8, 15, 6, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 28, 28, 65, 103, 201, 201, 201, 201, 201, 22, 22, 22, 22, 20, 20, 17, 17, 15, 8, 8, 1, 1, 1, 1, 22, 22, 22, 65, 65, 201] 201 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47]) total number of confs: 520 number of broken/clashed sets: 131 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242137 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242137 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242137/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242137 Building REAL300025242138 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242138' /scratch/stefan/7787021/working/building/REAL300025242138 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242138 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242138/0 /scratch/stefan/7787021/working/building/REAL300025242138 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1035) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1035 `/scratch/stefan/7787021/working/3D/1035' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1(C)CCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242138.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242138 none CC(CCNC(=O)C1(C)CCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 79, 92, 102, 113, 117, 117, 117, 201, 201, 201, 201, 201, 201, 55, 79, 25, 54, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 102, 102, 113, 113, 117, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 79, 79, 25, 25, 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: 801 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242138 none CC(CCNC(=O)C1(C)CCOCC1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 17, 23, 23, 31, 31, 59, 100, 201, 201, 201, 201, 201, 17, 17, 17, 17, 13, 13, 11, 11, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 59, 59, 201] 201 rigid atoms, others: [45, 11, 5, 38, 7, 8, 9, 10, 39, 12, 13, 44, 40, 43, 41, 42] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 46, 47, 48, 49, 50, 51]) total number of confs: 502 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242138 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242138 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242138/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242138 Building REAL300025242139 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242139' /scratch/stefan/7787021/working/building/REAL300025242139 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242139 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242139/0 /scratch/stefan/7787021/working/building/REAL300025242139 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1036) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1036 `/scratch/stefan/7787021/working/3D/1036' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(C)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242139.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242139 none CC(C)CC(C)CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 201, 70, 70, 70, 70, 70, 50, 49, 50, 37, 50, 26, 37, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 185, 185, 70, 70, 70, 70, 70, 50, 50, 50, 50, 50, 50, 50, 26, 26, 1] 201 rigid atoms, others: [55, 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, 51, 52, 53, 54]) total number of confs: 827 number of broken/clashed sets: 97 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242139 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242139 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242139/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242139 Building REAL300025242140 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242140' /scratch/stefan/7787021/working/building/REAL300025242140 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242140 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242140/0 /scratch/stefan/7787021/working/building/REAL300025242140 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1037) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1037 `/scratch/stefan/7787021/working/3D/1037' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)C(C)(C)C) `REAL300025242140.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242140 none CCC(CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1)C(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.3', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 170, 170, 170, 164, 150, 114, 92, 114, 62, 92, 26, 61, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 170, 164, 164, 150, 150, 114, 114, 114, 114, 92, 92, 92, 26, 26, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [49, 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, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 892 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242140 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242140 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242140/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242140 Building REAL300025242141 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242141' /scratch/stefan/7787021/working/building/REAL300025242141 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242141 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242141/0 /scratch/stefan/7787021/working/building/REAL300025242141 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1038) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1038 `/scratch/stefan/7787021/working/3D/1038' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1(C)CC(F)(F)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242141.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242141 none CC(CCNC(=O)C1(C)CC(F)(F)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [73, 64, 73, 80, 84, 84, 84, 84, 201, 201, 201, 201, 201, 201, 49, 64, 25, 48, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73, 80, 80, 84, 84, 84, 201, 201, 201, 201, 201, 201, 201, 64, 64, 64, 25, 25, 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: 645 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: REAL300025242141 none CC(CCNC(=O)C1(C)CC(F)(F)C1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 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: [14, 10, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 14, 18, 18, 24, 24, 50, 89, 201, 201, 201, 201, 201, 14, 14, 14, 14, 10, 10, 9, 9, 5, 2, 2, 2, 1, 1, 1, 1, 18, 18, 18, 50, 50, 201] 201 rigid atoms, others: [11, 5, 38, 7, 8, 9, 10, 39, 12, 13, 40, 41] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47]) total number of confs: 469 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242141 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242141 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242141/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242141 Building REAL300025242142 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242142' /scratch/stefan/7787021/working/building/REAL300025242142 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242142 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242142/0 /scratch/stefan/7787021/working/building/REAL300025242142 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1039) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1039 `/scratch/stefan/7787021/working/3D/1039' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)C1=CC2=C(CCC2)N1)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242142.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242142 none CC(CCNC(=O)C1=CC2=C(CCC2)N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 107, 123, 163, 183, 194, 194, 194, 201, 201, 201, 201, 201, 201, 201, 76, 107, 30, 76, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 163, 163, 183, 183, 194, 201, 201, 201, 201, 201, 201, 201, 201, 107, 107, 107, 30, 30, 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: 804 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: REAL300025242142 none CC(CCNC(=O)C1=CC2=C(CCC2)N1)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 20, 26, 26, 34, 34, 62, 101, 201, 201, 201, 201, 201, 20, 20, 20, 20, 15, 15, 12, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 62, 62, 201] 201 rigid atoms, others: [43, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46, 47, 48, 49]) total number of confs: 503 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242142 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242142 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242142/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242142 Building REAL300025242143 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242143' /scratch/stefan/7787021/working/building/REAL300025242143 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242143 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242143/0 /scratch/stefan/7787021/working/building/REAL300025242143 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1040) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1040 `/scratch/stefan/7787021/working/3D/1040' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=NOC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242143.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242143 none COCC1=NOC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 3, 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, 7] 0 hydrogens need 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, 154, 154, 154, 93, 93, 93, 82, 81, 52, 50, 52, 37, 50, 29, 37, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 154, 93, 82, 82, 81, 81, 52, 52, 52, 52, 50, 50, 50, 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: 787 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: REAL300025242143 none COCC1=NOC=C1C(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 3, 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, 7] 0 hydrogens 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, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 9, 9, 13, 13, 14, 14, 27, 27, 39, 63, 154, 154, 154, 154, 154, 8, 8, 8, 2, 2, 1, 4, 9, 9, 9, 9, 13, 13, 13, 13, 14, 14, 14, 39, 39, 154] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8] 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 375 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242143 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242143 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242143/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242143 Building REAL300025242144 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242144' /scratch/stefan/7787021/working/building/REAL300025242144 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242144 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242144/0 /scratch/stefan/7787021/working/building/REAL300025242144 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1041) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1041 `/scratch/stefan/7787021/working/3D/1041' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=N1) `REAL300025242144.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242144 none CC(C)N1C=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 73, 71, 47, 45, 47, 34, 45, 22, 34, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 87, 73, 73, 71, 71, 47, 47, 47, 47, 45, 45, 45, 22, 22, 1, 201] 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]) total number of confs: 537 number of broken/clashed sets: 93 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242144 none CC(C)N1C=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 1, 1, 1, 1, 5, 5, 5, 13, 13, 18, 18, 21, 21, 39, 39, 58, 93, 201, 201, 201, 201, 201, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 5, 13, 13, 13, 13, 18, 18, 18, 18, 21, 21, 21, 58, 58, 201, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 50, 25, 26] set([0, 2, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 515 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242144 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242144 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242144/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242144 Building REAL300025242145 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242145' /scratch/stefan/7787021/working/building/REAL300025242145 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242145 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242145/0 /scratch/stefan/7787021/working/building/REAL300025242145 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1042) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1042 `/scratch/stefan/7787021/working/3D/1042' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C)C=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)O1) `REAL300025242145.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242145 none CCC1=C(C)C=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 129, 129, 129, 126, 126, 126, 95, 95, 68, 57, 68, 44, 58, 29, 44, 13, 1, 1, 1, 1, 1, 1, 1, 129, 201, 201, 201, 201, 201, 129, 129, 129, 129, 126, 95, 95, 95, 95, 68, 68, 68, 68, 58, 58, 58, 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: 972 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: REAL300025242145 none CCC1=C(C)C=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 16, 16, 28, 28, 36, 54, 129, 129, 129, 129, 129, 1, 6, 6, 6, 6, 6, 2, 2, 2, 1, 3, 8, 8, 8, 8, 13, 13, 13, 13, 16, 16, 16, 36, 36, 129] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 35, 26] set([0, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 322 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242145 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242145 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242145/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242145 Building REAL300025242146 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242146' /scratch/stefan/7787021/working/building/REAL300025242146 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242146 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242146/0 /scratch/stefan/7787021/working/building/REAL300025242146 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1043) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1043 `/scratch/stefan/7787021/working/3D/1043' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)N=C1C) `REAL300025242146.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242146 none CC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)N=C1C 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 154, 144, 112, 74, 112, 59, 74, 37, 59, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 154, 154, 144, 144, 112, 112, 112, 112, 74, 74, 74, 37, 37, 1, 201, 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]) total number of confs: 879 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: REAL300025242146 none CC1=CC=C(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)N=C1C 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 4, 4, 3, 12, 16, 24, 24, 36, 36, 56, 56, 74, 111, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 4, 13, 13, 17, 17, 24, 24, 24, 24, 36, 36, 36, 74, 74, 201, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 560 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242146 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242146 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242146/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242146 Building REAL300025242147 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242147' /scratch/stefan/7787021/working/building/REAL300025242147 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025242147 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242147/0 /scratch/stefan/7787021/working/building/REAL300025242147 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1044) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1044 `/scratch/stefan/7787021/working/3D/1044' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CN1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242147.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242147 none CC1=CN=CN1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 141, 84, 84, 84, 82, 81, 80, 80, 80, 67, 80, 29, 67, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 141, 141, 84, 82, 82, 81, 81, 80, 80, 80, 80, 80, 80, 80, 29, 29, 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: 661 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: REAL300025242147 none CC1=CN=CN1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 201 conformations 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, 13, 13, 13, 15, 15, 16, 16, 16, 16, 21, 21, 55, 93, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 5, 5, 13, 15, 15, 15, 15, 16, 16, 16, 16, 16, 16, 16, 55, 55, 201] 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, 46, 47]) total number of confs: 478 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242147 /scratch/stefan/7787021/working /scratch/stefan/7787021 mkdir: created directory `1' /scratch/stefan/7787021/working/building/REAL300025242147/1 /scratch/stefan/7787021/working/building/REAL300025242147 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 1 (index: 1045) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1045 `/scratch/stefan/7787021/working/3D/1045' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C[NH+]=CN1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242147.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025242147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242147/1/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: REAL300025242147 none CC1=C[NH+]=CN1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 6, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 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, 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: [184, 184, 184, 184, 184, 184, 172, 124, 124, 124, 113, 113, 92, 66, 92, 66, 66, 33, 66, 13, 1, 1, 1, 1, 1, 1, 1, 184, 184, 184, 184, 184, 172, 172, 124, 113, 113, 113, 113, 92, 92, 92, 92, 66, 66, 66, 33, 33, 1] 184 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: 818 number of broken/clashed sets: 137 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242147 none CC1=C[NH+]=CN1CC(=O)NCCC(C)N(C)C(=O)CSC1=NNC(=O)[N-]1 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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 6, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 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, 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, 1, 1, 1, 1, 6, 15, 15, 15, 22, 17, 22, 22, 25, 25, 25, 25, 66, 96, 184, 184, 184, 184, 184, 2, 2, 2, 1, 1, 6, 6, 15, 22, 22, 22, 22, 22, 22, 22, 22, 25, 25, 25, 66, 66, 184] 184 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, 47, 48]) total number of confs: 505 number of broken/clashed sets: 137 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242147 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242147 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242147/0.* 1: /scratch/stefan/7787021/working/building/REAL300025242147/1.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242147 Building REAL300025242148 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242148' /scratch/stefan/7787021/working/building/REAL300025242148 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242148 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242148/0 /scratch/stefan/7787021/working/building/REAL300025242148 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1046) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1046 `/scratch/stefan/7787021/working/3D/1046' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)CCC(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025242148.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242148 none CC(CCNC(=O)CCC(F)F)N(C)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 5, 5, 15, 15, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 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, 7] 0 hydrogens 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, 80, 94, 102, 102, 102, 199, 198, 201, 201, 65, 76, 31, 64, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 80, 80, 94, 94, 102, 199, 199, 199, 199, 201, 76, 76, 76, 31, 31, 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: 889 number of broken/clashed sets: 125 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242148 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242148 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242148/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242148 Building REAL300025242149 mkdir: created directory `/scratch/stefan/7787021/working/building/REAL300025242149' /scratch/stefan/7787021/working/building/REAL300025242149 /scratch/stefan/7787021/working /scratch/stefan/7787021 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025242149 mkdir: created directory `0' /scratch/stefan/7787021/working/building/REAL300025242149/0 /scratch/stefan/7787021/working/building/REAL300025242149 /scratch/stefan/7787021/working /scratch/stefan/7787021 Protomer 0 (index: 1047) Found valid previously generated 3D confromation in /scratch/stefan/7787021/working/3D/1047 `/scratch/stefan/7787021/working/3D/1047' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=NOC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1) `REAL300025242149.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025242149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787021/working/building/REAL300025242149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242149 none CCOC1=NOC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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'] dock atom type numbers: [5, 5, 12, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 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, 7, 7] 0 hydrogens need 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, 199, 199, 199, 199, 199, 199, 199, 133, 133, 106, 75, 106, 60, 75, 41, 60, 13, 1, 1, 1, 1, 1, 1, 1, 199, 201, 201, 201, 201, 201, 199, 133, 133, 133, 133, 106, 106, 106, 106, 75, 75, 75, 41, 41, 1, 199] 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]) total number of confs: 833 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025242149 none CCOC1=NOC(C(=O)NCCC(C)N(C)C(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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'] dock atom type numbers: [5, 5, 12, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 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, 7, 7] 0 hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 13, 13, 17, 17, 38, 38, 62, 103, 199, 199, 199, 199, 199, 1, 6, 6, 6, 5, 5, 2, 7, 7, 7, 7, 13, 13, 13, 13, 17, 17, 17, 62, 62, 199, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 47, 26] set([0, 1, 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: 529 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787021/working/building/REAL300025242149 /scratch/stefan/7787021/working /scratch/stefan/7787021 Finished preparing REAL300025242149 Recording results /scratch/stefan/7787021/working /scratch/stefan/7787021 Appending to /scratch/stefan/7787021/finished/xaaabiq.* 0: /scratch/stefan/7787021/working/building/REAL300025242149/0.* Removing working files in /scratch/stefan/7787021/working/building/REAL300025242149 /scratch/stefan/7787021 Compressing combined databse files /scratch/stefan/7787021/finished/xaaabiq.db2.gz /scratch/stefan/7787021/finished/xaaabiq.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7787021/finished) ======================================================= Finalizing... removed `/scratch/stefan/7787021/working/3D/1048' removed directory: `/scratch/stefan/7787021/working/3D' `/scratch/stefan/7787021/working/protonate' -> `/scratch/stefan/7787021/archive' `/scratch/stefan/7787021/working/input-smiles.ism' -> `/scratch/stefan/7787021/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7787021/working/building' rmdir: removing directory, `/scratch/stefan/7787021/working' ls: No match. ls: No match.