VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 13 2006 - 15:56:25 CST

Hi Ivana,
  The APBS plugin in VMD 1.8.5 has a number of improvements which
you probably want, so as Axel already suggested, upgrading may be a good
idea unless you need to run VMD 1.8.4 for some other reason. As far as
finding the binary goes, so long as the APBS binary is called "apbs" and
is in your path, VMD should be able to find it automatically, if now, you
can tell VMD where to find it manually. The APBS plugin web page has
links to the main APBS page which contains tutorials and documentation
that should address your questions about the various parameters that
affect the electrostatics calculation. The VMD plugin doesn't do anything
special there other than provide an easy-to-use interactive interface to
the same set of parameters that one would normally write in the APBS job
configuration file. Let us know if you need more help getting this working.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Dec 13, 2006 at 03:15:09PM -0500, ivana adamovic wrote:
> Hi ,
>
> I am using VMD 1.8.4 and I have downloaded apbs-0.4.0. I have tried
> using APBS electrostatic tool to obtain electrostatic potential, but
> it didn't work ... VMD complained that it can't locate apbs. Also I am
> not quite sure about how to properly set up all parameters needed for
> this calculations. Is there an example somewhere?
>
> Thanks a lot,
>
> Ivana 

-- 
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