APBS XML parameter format — APBS-PDB2PQR 1.6 documentation

# APBS XML parameter format

This parameter file format has the following form:

    <ffname>
       <residue>
           <name>resname</name>
           <atom>
               <name>atomname</name>
               <charge>atomcharge</charge>
               <radius>atomradius</radius>
               <epsilon>atomepsilon</epsilon>
           </atom>
           ...
       </residue>
       ...
    </ffname>

The variables in this example are:

`ffname`
  The name of the forcefield. This is the root element of the XML file.
`resname`
  A string giving the residue name, as provided in the PDB file to be parameterized.
`atomname`
  A string giving the atom name, as provided in the PDB file to be parameterized.
`atomcharge`
  A float giving the atomic charge (in electrons).
`atomradius`
  A float giving the atomic Radius (in Å).
`atomepsilon`
  A float giving the Lennard-Jones well depth \(\epsilon\) (in kJ/mol). This is used for the calculation of WCA energies in apolar solvation energies and forces. We assume that the Lennard-Jones potential is defined in the “AMBER style”