From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 01 2012 - 11:47:43 CST
Hi,
Although we develop all of the VMD plugins here, I don't know much
about the details of how the Gromacs tools have been modified to be able
to use the VMD plugins from the point of view of a user.
If you don't get an answer here on VMD-L in the next day or two,
I would suggest that you ask this question on one of the Gromacs mailing
lists where there may be more people that know the answer.
Cheers,
John Stone
vmd_at_ks.uiuc.edu
On Wed, Feb 01, 2012 at 12:41:40PM -0500, PAUL NEWMAN wrote:
> Dear NAMD and VMD users,
>
> I want to use the Gromacs analysis tools for analyzing Namd output files
> (*.dcd files) I just installed Gromacs 4.5.4 and it works well. In
> addition I installed VMD 1.9 and set up
> VMD_PLUGIN_PATH=/home/vmd-1.9/plugins/LINUXAMD64/molfile/ (Here it is
> located the dcdplugin.so )
> I verified that VMD_PLUGIN_PATH is pointing out to the right folder.
> However when I run for example
>
> g_rmsf_d -f file.dcd -s file.pdb
>
> I got the following error
>
> The file format of file.dcd is not a known trajectory format to GROMACS.
> Please make sure that the file is a trajectory!
>
> GROMACS will now assume it to be a trajectory and will try to open it
> using the VMD plug-ins.
> This will only work in case the VMD plugins are found and it is a
> trajectory format supported by VMD.
>
> No plugin for dcd found
>
> Am I doing something wrong? Do I need to do something else?
>
> Any help and advise will be highly appreciate it
>
> Thanks so much for the help
>
> --
> Cheers,
>
> Paul
-- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
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