VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 23 2003 - 10:23:09 CST

Dear Vlad,
  There are two VMD scripts available which may be of interest to you
since you have access to Delphi. One is "potsel" which calculates
potential for an atom selection in VMD, and the other is "potsurf"
which colors a surface representation in VMD by the potential values
supplied by Delphi. These two scripts should be a good starting point
for you to get VMD working with Delphi.

The two scripts are here:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/potsel/
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/potsurf/

Along the same lines, I believe that Nathan Baker's APBS package
comes with some scripts to allow it to work with VMD.
It is available for free, and they've got a web portal setup for
running jobs on the NPACI machines:
  http://agave.wustl.edu/apbs/

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jan 23, 2003 at 05:08:51PM +0100, Vlad Cojocaru wrote:
> Dear Friends,
> I have run Delphi jobs and I got ".phi" files. I also got from
> Delphi runs a files "data", "ARCDAT". Could somebody explain very
> shortly something about "data" and "ARCDAT"files? Also I would like to
> visualize the electrostatic potential calculated using VMD, gOPENMOL or
> some other software. Could somebody give some hints about how to do that?
>
> For vmders,
> Is VMD able to do this type of job or shell I use something else? I
> do not have installed Delphi on the machine that I want to visualize the
> data so dont know if the scripts from the library are applicable. All
> that I have is the output files from Delphi.
>
> Thanks a lot in advance for any kind of help,
> Best regards,
> vlad
>
> --
> Vlad Cojocaru
> Max Planck Institute for Biophysical Chemistry
> Department: 060
> Am Fassberg 11, 37077 Goettingen, Germany
> tel: ++49-551-201.1327
> e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
> home tel: ++49-551-9963204
>
> 

-- 
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