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Can I add my own charge and radius parameters to PDB2PQR?

Yes; there are two ways to add your own parameters to PDB2PQR:

Adding a few additional parameters to an existing forcefield

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 (dat/AMBER.DAT) directly and add your parameters. After the parameter addition, save the force field data file (dat/AMBER.DAT) 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

If you are adding a new forcefield to PDB2PQR, then you will need to follow the instructions below:
  1. Provide two files:
    • Your forcefield data file (e.g., myff.DAT).
    • If your atom naming scheme of the forcefield is different from the PDB2PQR canonical naming scheme, then you will also need to provide a names files (myff.names). It is recommended to build your own forcefield data file and names file based on existing .DAT and .names file formats. For more information on the XML format used in .names files, please refer to the XML file format documentation.
  2. 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:
    • For command line execution:
      1. Locate your PDB2PQR distribution and place the forcefield and names files in the dat/ directory.
      • On PDB2PQR command line version, run: python pdb2pqr.py [options] --ff=myff {path} {output-path}
    • For the web server, select "User-defined forcefield" radio button, then specify your user-defined data file and names file. Select other options when needed, and then click "Submit".
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