Thread: [Apbs-users] Ligand parametrization
Biomolecular electrostatics software
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From: George T. <gtz...@ma...> - 2009-07-29 13:00:27
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Hi everybody, I'm trying to convert a docked ligand conformation from pdb to pqr format. The ligand is an 18 C-atom hydrocarbon with two double bonds in positions 10 and 12 and a carboxylic acid end. I'm using the following terminal command: $ python pdb2pqr.py --ff=amber --ligand=ligand.mol2 ligand.pdb result.pqr This command works find for non-carboxylated ligands. However, for the ligand described above I get the following error message: WE MATCHED acetylsalicylicacid matchedligatoms : ['OAI', 'OAH', 'CAG', 'CAF', 'CAB', 'CAD', 'CAC', 'CAA', 'CAE'] type : Carboxylic_Acid modelpka : 4.99 titratableatoms : ['OAH', 'OAI', 'CAG', 'CAB', 'CAC', 'CAD', 'CAE', 'CAF'] matching atoms : {'C80': 'CAD', 'C': 'CAG', 'C40': 'CAF', 'C50': 'CAC', 'C60': 'CAE', 'C30': 'CAB', 'O2': 'OAI', 'O1': 'OAH'} {'titratableatoms': ['OAH', 'OAI', 'CAG'], 'matching_atoms': {'C': 'CAG', 'O2': 'OAI', 'O1': 'OAH'}, 'templatename': 'AceticAcid', 'modelpka': 4.7999999999999998, 'matchedligatoms': ['OAI', 'OAH', 'CAF', 'CAG'], 'type': 'Carboxylic_Acid'} Traceback (most recent call last): File "pdb2pqr.py", line 63, in <module> mainCommand(sys.argv) File "/Users/george1/pdb2pqr/main.py", line 567, in mainCommand header, lines, missedligands = runPDB2PQR(pdblist, ff, options) File "/Users/george1/pdb2pqr/main.py", line 350, in runPDB2PQR Lig.make_up2date(residue) File "/Users/george1/pdb2pqr/pdb2pka/ligandclean/ligff.py", line 283, in make_up2date xxnetqxx = xxnetqxx+aa.charge TypeError: unsupported operand type(s) for +: 'float' and 'str' Any help would be greatly appreciated. Best regards George |