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 (
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
.names examples provided with PDB2PQR in the
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.