This parameter file format has the following form:
The variables in this example are:
- Any number of comment lines, each line starting with the "#" symbol. This is not valid XML syntax...
- The name of the forcefield. This is the root element of the XML file.
- A string giving the residue name, as provided in the PDB file to be parameterized.
- A string giving the atom name, as provided in the PDB file to be parameterized.
- 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":