VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 23 2003 - 14:37:36 CST

I thought I'd forward this tip from Rui, regarding using Delphi 4 rel 1.1
with the VMD scripts in the script library. Anyone know if its possible
to detect which version of delphi made the files?

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

----- Forwarded message from "J. Rui Rodrigues" <jrui_at_ci.uc.pt> -----

Date: Thu, 23 Jan 2003 20:23:21 -0000
To: "John Stone" <johns_at_ks.uiuc.edu>
Subject: Re: visualizing Delphi output (electrostatic potential)
From: "J. Rui Rodrigues" <jrui_at_ci.uc.pt>

Hi,
Just to tell you that those scripts are not compatible with delphi 4 release
1.1 as the format for the delphi params file seems to have changed... The
scripts should be edited, changing lines

puts $paramFile "$igrid"
puts $paramFile "60"
..

to
puts $paramFile "GSIZE=$igrid"
puts $paramFile "PERFIL=60"
..

Best regards,
Rui Rodrigues

John Stone <johns_at_ks.uiuc.edu> escreveu:

> 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
> 

-- 
J. Rui Rodrigues
Dep. de Quimica
----- End forwarded message -----
-- 
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