VMD-L Mailing List

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Wed Nov 24 2004 - 10:13:23 CST

Are the permissions on that directory set so that vmd can have read/write
access?

Brian

On Tue, 23 Nov 2004, 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
>
>
>

*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
*****************************************************************