Hi Jack, > In all of the examples distributed with APBS, the pdie (solute dielectric)
The pdie must be the protein dielectric constant though the comment for pdie in the pymol generated .in-file reads "# Solute dielectric" ... that is probably a mistake. The APBS-plugin says Protein Dielectric. The protein and solvent dielectric constants as well as the ionic strenth of the solute influences the electrostatic potentials so you need to select appropriate values. I can't tell you how to do that, since I simply rely on what other people have used for the protein I work with (blood coagulation factor V) - I use a protein dielectric constant of 4 and solute dielectric constant of 80. Regards, ./ Kristoffer
