This parameter file format has the following form:

   # Comments	
   <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:

Comments

Any number of comment lines, each line starting with the "#" symbol. This is not valid XML syntax...

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  (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":