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”