Extending PDB2PQR

Adding new forcefield parameters

If you are just adding the parameters of a few residues and atoms to an existing forcefield (e.g., AMBER), you can open the forcefield data file distributed with PDB2PQR (dat/AMBER.DAT) directly and add your parameters. After the parameter addition, save the force field data file with your changes. You should also update the corresponding .names file (dat/AMBER.names) if your added residue or atom naming scheme is different from the PDB2PQR canonical naming scheme.

Adding an entirely new forcefield

The following steps outline how to add a new force field to PDB2PQR.

You will need to generate a forcefield data file (e.g., myff.DAT) and, if your atom naming scheme of the forcefield is different from the PDB2PQR canonical naming scheme, you will also need to provide a names files (myFF.names). The format of the names file is described in PDB2PQR NAMES files. It is recommended to build your own forcefield data and names files based on existing PDB2PQR .DAT and .names examples provided with PDB2PQR in the dat directory. After finishing your forcefield data file and names file, these can be used with either the command line or the web server versions of PDB2PQR.

Helping with development

Adding new functionality

PDB2PQR welcomes new contributions; the software API is documented in API Reference. To contribute code, submit a pull request against the master branch in the PDB2PQR repository. Please be sure to run PDB2PQR tests, as described in Testing, before submitting new code.

Helping with to-do items

A list of “to-do” items for the code is available in GitHub Issues. A loosely maintained list auto-generated from the documentation is also presented below.


This code should be moved to the APBS code base.

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs-etl/checkouts/latest/pdb2pqr/psize.py:docstring of pdb2pqr.psize, line 3.)