VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 19 2002 - 15:16:54 CDT

Hi Surjit,

On Thu, Sep 19, 2002 at 03:35:46PM -0400, Surjit Dixit wrote:
> Hi,
> I have a CD with a trajectory and parameter topology file (AMBER format)
> burnt on a Windows machine.
> I am able to view this trajectory with VMD on Windows machines but VMD
> on linux crashes when I
> try to read these files. ptraj, another program in Amber suite also has
> problems reading these files, so something
> is surely wrong with the file.

If VMD can read the file correctly on Windows, then it must be some
other problem. Since I assume you're running Linux on the same machine,
then its not an endianism problem, it might be some other strange issue.
What type of machine was the original AMBER simulation run on?
Was it on a Windows machine or on Unix? This makes a difference.

> Both of these are text files.

I suspected that this is a problem with CR/LF handling in
both VMD and ptraj, even before I read this comment, now its
almost assuredly the cause.

> If I copy(ftp) these same files from the linux machine to another
> windows machine, VMD reads the files neatly
> on windows. I am able to read this files with vi editor on the linux
> machine and both of them look normal. I thought it might be
> something to do with the end of line problem because of the dos->unix
> movement but but viewing it in vi, I am not able
> to detect anything abnormal about these files.

Yes, I believe this is exactly the problem.

> I know this is not a VMD problem, but thought somebody on the list might
> have some ideas about the source of such
> a problem. I am running out of ideas and would appreciate any help.

How big is the file?
If you can provide us with a copy of the file (or one like it) I bet
we can fix VMD so it is immune to the CR/LF problems. We've run into
similar issues with text files on Windows, Mac, and Unix, as all three
platforms use a different CR/LF end of line convention.
If you've got a small example that exhibits the problem, I can give you
an FTP area to upload it and we can try to do something about this in
the VMD file reader plugins for the old revs of AMBER.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu 

-- 
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