VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 23 2004 - 13:22:48 CDT

Hi,
  If you're running VMD in a truly batch mode, redirecting stdin from your
script and stdout to a file or /dev/null, you can use the -eofexit option.
Alternately, if you're careful to use the waitfor all option in your molecule
loading commands, or you use -dispdev text, you should be able to simply
add "exit" to the end of your script. Some of this is discussed in the
User's Guide section on command line options where -eofexit is mentioned.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Sep 23, 2004 at 10:55:09AM -0700, mdcooper wrote:
> Hi all,
>
> I know this may seem much too easy, but I am having a surprisingly hard time
> finding the answer.
>
> I want to run an automated batch file which utilises VMD to set occupancy
> values.
>
> I want to run a simple .pgn file:
>
> set allatoms [atomselect top all]
> set ligand [atomselect top "resname NAD"
> $allatoms set occupancy 0
> $ligand set occupancy 1
> $allatoms writepdb ".\\working\\smd.ref"
> quit
>
> and then have vmd quit so that the batch file may continue. I just cannot
> figure out how to make VMD quit automatically.
>
> Thanks,
>
> Matt
> 

-- 
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