[gmx-users] Fwd: electrostatic potential map

[tarak karmakar]

Thanks
I have little more confusion about the charges assigned to each of the
atoms from pdb2pqr. With and without water the charges of all the protein
atoms are same! But, then why this type of discrepancy is coming from the
potential map?

Thanks for giving the apbs mailing list address. I'll post there, from now
onwards.


On Tue, May 14, 2013 at 11:41 PM, andrew ritchie
<drew.w.ritchie at gmail.com>wrote:

> Tarak,
>
> 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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