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/7795224/working' mkdir: created directory `/scratch/stefan/7795224/working/protonate' Storing results in /scratch/stefan/7795224/finished Working in /scratch/stefan/7795224/working /scratch/stefan/7795224/working /scratch/stefan/7795224 /scratch/stefan/7795224/working/protonate /scratch/stefan/7795224/working /scratch/stefan/7795224 Precomputing protomers for all compounds (pH: 7.4) rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: `/nfs/home/stefan/.install4j_new' and `/nfs/home/stefan/.install4j' are the same file mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory ph 7.4: 2 protomers created Coalesing and merging protomers 2 protomers generated for 2 compounds Checking for new stereocenters and expanding 2 protomers after new stereo-center expansion /scratch/stefan/7795224/working /scratch/stefan/7795224 Bulk generating 3D conformations all protomers in /scratch/stefan/7795224/working/3D mkdir: created directory `/scratch/stefan/7795224/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7795224/working/protonate/xaaaaaa-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' 3 3D conformations generated for 2 compounds Building REAL300024332853 mkdir: created directory `/scratch/stefan/7795224/working/building' mkdir: created directory `/scratch/stefan/7795224/working/building/REAL300024332853' /scratch/stefan/7795224/working/building/REAL300024332853 /scratch/stefan/7795224/working /scratch/stefan/7795224 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024332853 mkdir: created directory `0' /scratch/stefan/7795224/working/building/REAL300024332853/0 /scratch/stefan/7795224/working/building/REAL300024332853 /scratch/stefan/7795224/working /scratch/stefan/7795224 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7795224/working/3D/1 `/scratch/stefan/7795224/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(NC(=O)CC2=NC(=O)O[N-]2)C(=O)N(C2=CC=CC=C2)N1C) `REAL300024332853.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024332853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7795224/working/building/REAL300024332853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024332853 none CC1=C(NC(=O)CC2=NC(=O)O[N-]2)C(=O)N(C2=CC=CC=C2)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 5, 1, 8, 1, 11, 12, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 8, 8, 8, 41, 141, 141, 141, 141, 141, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 8, 41, 41, 3, 3, 3, 3, 3, 2, 2, 2] 141 rigid atoms, others: [0, 1, 2, 3, 13, 14, 15, 16, 22, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024332853 none CC1=C(NC(=O)CC2=NC(=O)O[N-]2)C(=O)N(C2=CC=CC=C2)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 5, 1, 8, 1, 11, 12, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 56, 56, 8, 56, 1, 1, 1, 1, 1, 1, 1, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 56, 8, 8, 141, 141, 141, 141, 141, 141, 141, 141] 141 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 261 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: REAL300024332853 none CC1=C(NC(=O)CC2=NC(=O)O[N-]2)C(=O)N(C2=CC=CC=C2)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 5, 1, 8, 1, 11, 12, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 14, 14, 14, 71, 141, 141, 141, 141, 141, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 14, 71, 71, 1, 1, 1, 1, 1, 3, 3, 3] 141 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37]) total number of confs: 357 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7795224/working/building/REAL300024332853 /scratch/stefan/7795224/working /scratch/stefan/7795224 Finished preparing REAL300024332853 Recording results /scratch/stefan/7795224/working /scratch/stefan/7795224 mkdir: created directory `/scratch/stefan/7795224/finished' Appending to /scratch/stefan/7795224/finished/xaaaaaa.* 0: /scratch/stefan/7795224/working/building/REAL300024332853/0.* Removing working files in /scratch/stefan/7795224/working/building/REAL300024332853 Building REAL300024332854 mkdir: created directory `/scratch/stefan/7795224/working/building/REAL300024332854' /scratch/stefan/7795224/working/building/REAL300024332854 /scratch/stefan/7795224/working /scratch/stefan/7795224 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024332854 mkdir: created directory `0' /scratch/stefan/7795224/working/building/REAL300024332854/0 /scratch/stefan/7795224/working/building/REAL300024332854 /scratch/stefan/7795224/working /scratch/stefan/7795224 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7795224/working/3D/2 `/scratch/stefan/7795224/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(NC(=O)OC(C)(C)C)C2=NC(=O)O[N-]2)C=C1) `REAL300024332854.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024332854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7795224/working/building/REAL300024332854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024332854 none COC1=CC=C(C(NC(=O)OC(C)(C)C)C2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 38, 64, 64, 84, 85, 85, 85, 13, 67, 67, 67, 67, 67, 1, 1, 2, 2, 2, 1, 1, 13, 38, 85, 85, 85, 85, 85, 85, 85, 85, 85, 1, 1] 135 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 40, 21, 22, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 326 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024332854 none COC1=CC=C(C(NC(=O)OC(C)(C)C)C2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [67, 34, 33, 67, 67, 13, 1, 13, 46, 71, 71, 88, 90, 90, 90, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 67, 67, 13, 46, 90, 90, 90, 90, 90, 90, 90, 90, 90, 67, 67] 135 rigid atoms, others: [6, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 459 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7795224/working/building/REAL300024332854 /scratch/stefan/7795224/working /scratch/stefan/7795224 Finished preparing REAL300024332854 Recording results /scratch/stefan/7795224/working /scratch/stefan/7795224 Appending to /scratch/stefan/7795224/finished/xaaaaaa.* 0: /scratch/stefan/7795224/working/building/REAL300024332854/0.* Removing working files in /scratch/stefan/7795224/working/building/REAL300024332854 /scratch/stefan/7795224 Compressing combined databse files /scratch/stefan/7795224/finished/xaaaaaa.db2.gz /scratch/stefan/7795224/finished/xaaaaaa.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7795224/finished) ======================================================= Finalizing... removed `/scratch/stefan/7795224/working/3D/3' removed directory: `/scratch/stefan/7795224/working/3D' rmdir: removing directory, `/scratch/stefan/7795224/working/building' rmdir: removing directory, `/scratch/stefan/7795224/working' ls: No match. ls: No match.