APBS flat-file parameter format — APBS-PDB2PQR 1.6 documentation

# 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”