Ok, but if I am to prepare the PQR file manually, where do I get the charges and radii for the ligand, required by the PQR format?
This depends on what kind of ligand that is. For ions, or something very simple like water, the best way is to take these from the AMBER data base. We are also building a data-base of PQR files for more complex ligands, see here . For other ligands, you will most likely need to compute charges from scratch, unless you have access to pre-computed ones for your specific ligand. H++ users have reported using PRODRG2 server for the purpose. Ideally, you would want to perform a high quality QM calculation followed by a charge fitting procedure such as RESP. As for the radii, these follow a very simple pattern, see any PQR file generated by H++ (currently, Bondi set is used). When constructing a PQR file, always remember to separate different chain records by a “TER”, and put a “TER” in the end as well to let H++ know which residues should be treated as terminal.
