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:
- A string giving the residue name, as provided in the PDB file to be parametrized.
- A string giving the atom name, as provided in the PDB file to be parametrized.
- A float giving the atomic charge (in electrons).
- A float giving the atomic radius (in Å).
- 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”