Editing APBS Electrostatics Plugin (section)

=== Prepare Molecule ===

APBS requires '''partial charges''' and '''atom radii'''. Since PDB files
don't provide this information, they have to be preprocessed first.

'''pdb2pqr''' is the default preparation method, it is limited to protein and
nucleic acid, unless the user provides his own forcefield parameters.

The '''prepwizard''' method is available if the user has the
[https://schrodinger.com Schrodinger Suite]
installed. It can handle a variety of molecules.

You can also use any '''third-party tool''' that assigns partial charges
and load the result into PyMOL. Supported file formats include PQR, MOL2, and MAE.
In that case, uncheck "Prepare Molecule", or use
"Method: use vdw" if you only have charges but no radii.
Tools to consider are for example [http://openbabel.org/ Open Babel]
or the [http://www.poissonboltzmann.org/ PDB2PQR web server].