how should I interpret the final potential that I got from APBS after setting the dielectric constant of the solvent equal to the dielectric constant of the solute =2?
Would this give me a course representation of the potential inside the molecule due to redistribution of the charges via e.g. covalent bonds (if initially AMBER force field is used in pdb2pqr)? Is this redistribution between a small groups of atoms (residues).
thank you a lot