[gmx-users] Fwd: electrostatic potential map

andrew ritchie drew.w.ritchie at gmail.com
Tue May 14 20:11:48 CEST 2013


That's more of a question for the APBS mailing list, but I'll give it my
best shot, but I would highly suggest you check out
http://www.poissonboltzmann.org/apbs first.

APBS is an implicit solvent electrostatics model, and as such you should be
careful with what explicit solvent you include, ie: water that behaves as
bulk water should probably not be explicitly included in the calculation,
while a water molecule that is persistently hydrogen-bonding to a region of
your protein may better be modeled explicitly.  Including waters may change
the molecule surface definitions (based on the atom radii given to the
water molecule atoms), which will change where the high/low dielectric
boundary occurs.

Water's role in the calculation is the same as any other point charge's
role in the calculation--given a charge and radius, the potential obeys the
Poisson-Boltzmann equation.  The Poisson-Boltzmann equation doesn't care
that the atoms are part of water molecules, it just cares about the charge
on the atoms, the size of the atom (because the atom charges are mapped to
grid points in the system based on the size), and the dielectric of the
region the atom is in.

I hope this was a little bit helpful,
-Andrew Ritchie
The University of Texas at Austin
Department of Chemistry and Biochemistry
The Webb Group

On Mon, May 13, 2013 at 7:04 AM, tarak karmakar <tarak20489 at gmail.com>wrote:

> Dear All,
>      I am running a simulation of ligand binding in a protein. Ligand is
> mostly negatively charged, so as expected it should bind to the positive
> region of the protein. To check the possible binding zone, I try to
> calculate or rather visualize the electrostatic potential map of a protein
> in PYMOL. In this context I am utilizing pdb2pqr and then APBS in PYMOL.
> Surprisingly, I see two different types of pictures, in presence and in
> absence of water molecules present in the protein pdb file. In presence of
> water molecules, some regions in the protein are showing positive while in
> absence of water molecules these (same) regions are showing negative
> potential. I don't know, exactly, what is the effect of water molecules in
> this calculations.
>     Any short of suggestions would be greatly appreciated. ( I apologize
> for posting bit different topic in this mailing list)
> Thanks and regards,
> Tarak
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-Andrew Ritchie

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