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
issue before?
Jack
