Re: [AMBER] counterions placings

From: Jason Swails <>
Date: Fri, 9 Jul 2010 10:48:22 -0400

At infinite distance, the system merely looks like a point charge with the
charge of the net charge of the molecule, so there will be no electric field
for a formally neutral protein. However, that doesn't mean that the ESP is
0 close to the protein where the point charge model is invalid.

If you want to take a look at the ESP, you can use a program like apbs or
some other PB solver. VMD has an apbs plugin that will allow you to plot
and visualize the electrostatic potential, and that should convince you that
infinite distance is NOT the ideal location for ions according to this

Hope this helps,

On Fri, Jul 9, 2010 at 2:46 AM, Jio M <> wrote:

> Dear AMBER users,
> I am not able to understand meaning of "points of lowest/highest
> electrostatic potential" where counter charge is placed in
> Actually confusion is V inversely related to r and if net system charge is
> +q then only at infinite V will be minimum that is zero.....(I read it at
> 1) so does counterion is placed at farthest position always? but it seems
> some problem in my understanding of the concept
> 2) "Calculating grid charges" is displayed when addions is used..somebody
> please explain why this is required... or source from where I can know how
> calculations being done or atleast philosophical concept....
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Fri Jul 09 2010 - 08:00:04 PDT
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