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”