VMD-L Mailing List

From: ivana adamovic (iadamovic_at_gmail.com)
Date: Tue Feb 28 2006 - 09:47:44 CST

Thanks a lot for such a quic answer.

I'll look through it some more.

Ivana

On 2/27/06, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> VMD doesn't do any PB calculations internally, but we include a plugin
> that helps setup and run APBS jobs from molecules loaded in VMD.
> http://www.ks.uiuc.edu/Research/vmd/plugins/apbsrun/
>
> Also, there's a PME potential plugin that may be of interest if you
> want to know what potentials NAMD is using for periodic simulations
> using PME:
> http://www.ks.uiuc.edu/Research/vmd/plugins/pmepot/
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Feb 27, 2006 at 01:19:48PM -0500, ivana adamovic wrote:
> > Hello,
> >
> > I am quite new in using VMD, so I hope that this question was not answered
> > already, if so, please just point me to where the solution of the problem
> > was already described.
> >
> > I would appreciate help on how to obtain electrostatic potential map using
> > VMD. Can it run PB calculations or we need to read in files form some of the
> > MD codes?
> >
> > What is done in APBS Electrostatic part of the Analysis section and in PME ?
> >
> > Could you explain me a set up for both of these parts?
> >
> > Thanks a lot,
> >
> > Ivana Adamovic
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>