VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Nov 24 2004 - 09:51:44 CST

Luis,
  Have you actually run that MSMS binary by hand yet? It is possible
that the MSMS binary you have isn't executing for some reason (mismatched
shared library versions, or something, sometimes occurs). If you can run
it by hand succesfully, let me know and I'll help you figure out what's
going on there. Do you have "localhost" defined in your /etc/hosts file
on Linux? That's often the other thing that causes MSMS to fail.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Nov 23, 2004 at 06:52:35PM -0600, Luis Rosales wrote:
>
> Hi all:
>
> A really basic question:
> I am setting vmd to work with msms, so I had put on my vmd script
>
> # find where the MSMS executable is located
> if ($?MSMSSERVER == "0") then
> setenv MSMSSERVER "/home/arioco/bin/MSMS/msms.i86Linux2.2.5.5"
> endif
>
> However, vmd is unable to call msms and I got the following message:
>
> Info) Finished with coordinate file bin/MSMS/1crn.pdb.
> Info) Starting MSMS with: '/home/arioco/bin/MSMS/msms.i86Linux2.2.5.5
> -no_area -socketPort 1357 &'
> Info) Waiting for MSMS server ...
> Info) Waiting for MSMS server ...
> Info) Waiting for MSMS server ...
> Info) Waiting for MSMS server ...
> ERROR) Could not connect to MSMS server. Please check that the program
> '/home/a
> rioco/bin/MSMS/msms.i86Linux2.2.5.5' exists and is executable, or set the
> environment variable MSMSSERVER to point to the correct binary.
> Info) Could not compute MSMS surface
> Info) Done with MSMS surface.
>
> My msms binary is called msms.i86Linux2.2.5.5 and is in the path
> /home/arioco/bin/MSMS/ and I could run msms from the command line,
>
> Any ideas about what I am missing???
>
> Thanks,
>
> Luis
>
> 

-- 
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