Flat-file parameter format

This parameter file format is a series of lines of the form:

   Residue_name Atom_name Charge Radius Epsilon

where the whitespaces are important and denote separation between the fields. The fields here are:

Residue_name: A string giving the residue name, as provided in the PDB file to be parametrized.
Atom_name: A string giving the atom name, as provided in the PDB file to be parametrized.
Charge: A float giving the atomic charge (in electrons).
Radius: A float giving the atomic radius (in Å).
Epsilon: A float giving the Lennard-Jones well depth $ε$ (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":

$U_{\mathrm{LJ}}(r) = \epsilon \left( \left( \frac{\sigma}{r} \right)^{12} - \left( \frac{\sigma}{r} \right)^6 \right)$