APBS 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 (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”