I have stumbled across the parameter causing the difference.
In all of the examples distributed with APBS, the pdie (solute dielectric)
value is set to 2.0 whereas ABPS-tools.py defaults this to 20.0. I find
that if I use 2.0 instead of 20.0 for pdie, the resulting electrostatic
potential map is much more similar to what GRASP generates. Now I have a
few pools of positive charge remaining whereas before the entire molecule
(-15 net charge) had a negative surface. Has anyone else noticed this
> 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.
Get latest updates about Open Source Projects, Conferences and News.