VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 12 2006 - 10:07:41 CST

Syma,
  Your script isn't closing the output file when it finishes, which may
explain why you're getting random incomplete output. You need to add:
  close $outfile

To the end of your script.

Also, if you're running the script in batch mode as part of a larger
script the loads the files etc, you'll need to make sure that you use
the "waitfor all" option when loading trajectory data with "mol new" or
"mol addfile" so that VMD doesn't allow your script to continue until
all of the trajectory frames are loaded.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jan 12, 2006 at 04:03:02PM -0000, syma wrote:
> Hi,
>
> I have attached a script I use to work print out the number of lipid-protein
> contacts and the coordinates of the lipid atom involved in the contact for
> each frame of a trajectory. This seemed to be working ok when I was looking
> for large numbers of contacts, eg the whole protein. However when I try to
> analyse contacts for only selected protein residues, the script doesn't read
> all the frames/write output for all frames in the trajectory and stops at
> what seem like arbitrary points.
>
>
> Please could you help me to identify the cause of this?
>
> Thanks in advance for your help.
>
> -Syma
>
> ***************************************************
>
> Dr Syma Khalid
> Department of Biochemistry,
> University of Oxford
> South Parks Road,
> Oxford
> OX1 3QU
> U.K.
>
>
>
> ***************************************************
>
> 

-- 
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