sobolevnrm
commented
2 months ago Unfortunately, this is likely a limitation of the program.
Open and-tos opened 2 months ago
sobolevnrm
commented
2 months ago Unfortunately, this is likely a limitation of the program.
I am getting the following error when trying to assign protonation states to PDB 3ptg along with the ligand. Am I doing something wrong or is this just a limitation of the program?
INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO:Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO:Checking and transforming input arguments. INFO:Loading topology files. INFO:Loading molecule: 3ptg.pdb INFO:Setting up molecule. Traceback (most recent call last): File "/usr/local/bin/pdb2pqr30", line 8, in <module> sys.exit(main()) File "/usr/local/lib/python3.8/dist-packages/pdb2pqr/main.py", line 829, in main if main_driver(args) == 1: File "/usr/local/lib/python3.8/dist-packages/pdb2pqr/main.py", line 771, in main_driver biomolecule, definition, ligand = setup_molecule( File "/usr/local/lib/python3.8/dist-packages/pdb2pqr/main.py", line 404, in setup_molecule ligand.read(ligand_file) File "/usr/local/lib/python3.8/dist-packages/pdb2pqr/ligand/mol2.py", line 458, in read mol2_file = self.parse_bonds(mol2_file) File "/usr/local/lib/python3.8/dist-packages/pdb2pqr/ligand/mol2.py", line 551, in parse_bonds raise NotImplementedError( NotImplementedError: PDB2PQR does not currently support the amide (am) bond type.