VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 27 2006 - 16:06:56 CST

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
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