[Apbs-users] Surface definition

[Vladimir L. <vla...@gm...>]

Hi all,

I am doing electrostatic calculations using APBS, and was wondering how does
APBS defines the surface of the molecules? Looking for the answer I read
some of M. Holst's PhD work, where he divides the simulation box into three
regions: 1 - the protein, 2 - a layer of solvent that does not have any
mobile charges and 3 - the solvent with ions. I was wondering if the same
principles are implemented in APBS, if so, then how does APBS calculates
width of the region 2. Also how does APBS define the surface of the
molecule? Is it just using the radii specified in the .pqr files?
Also, if I were to specify some atom with the radius 1, and the epsilon for
my protein was 2, then the epsilon inside the sphere of radius 1 around this
atom would be 2, or how does assigning the dielectric constant works in
APBS?

Thank you very much.

Vladimir