APBS XML parameter format¶
This parameter file format has the following form:
<ffname>
<residue>
<name>resname</name>
<atom>
<name>atomname</name>
<charge>atomcharge</charge>
<radius>atomradius</radius>
<epsilon>atomepsilon</epsilon>
</atom>
...
</residue>
...
</ffname>
The variables in this example are:
ffname
- The name of the forcefield. This is the root element of the XML file.
resname
- A string giving the residue name, as provided in the PDB file to be parameterized.
atomname
- A string giving the atom name, as provided in the PDB file to be parameterized.
atomcharge
- A float giving the atomic charge (in electrons).
atomradius
- A float giving the atomic Radius (in Å).
atomepsilon
- 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”