APBS 0.4.0 User Guide: Adaptive Poisson-Boltzmann Solver
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Parameter file format

APBS uses a very simple format for parameter files to be used with the READ parm command. The parameter file is a series of lines of the format:


        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 parameterized.

Atom_name

A string giving the atom name, as provided in the PDB file to be parameterized.

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 (in kcal/mol); this parameter is read but not currently used by APBS.

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