[gmx-users] How to set the VMD_PLUGIN_PATH for gromacs analysis?

[Roland Schulz]

Hi,

please make sure you compile with support for vmd plugins. One way to check
is that the src/config.h in your build folder contains "#define
GMX_DLOPEN". If it does not please check for warnings/errors in the
cmake/configure output and let us know how you run cmake/configure.

If have compiled with  vmd plugin support, please send the full output of
the tool and please send me a small trajectory which reproduces the
problem.

Roland

On Fri, Mar 30, 2012 at 11:47 PM, a a <patd_2 at hotmail.com> wrote:

>  Dear Sir/Madam,
>
>
> I am trying to run covar using mdcrd file.
>
>
> I installed the vmd and gromacs 4.5.5. to my computer. I also set the VMD_PLUGIN_PATH by adding a line in .bashrc file in my home directory.
>
>
> VMD_PLUGIN_PATH=/home/cmche/AnnieSoftwares/vmd_ie
>  d/lib/vmd/plugins/LINUX/molfile
>
>
> When I did the following command:
>
> /usr/local/gromacs/bin/g_covar_d -s average.pdb -f md0.mdcrd -o -v
>
>
>  I get the following error message.
>
>
> -------------------------------------------------------
> Program g_covar_d, VERSION 4.5.5
> Source code file: trxio.c, line: 870
>
> Fatal error:
> Not supported in read_first_frame: md0.mdcrd
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
>
>  Thanks to Francesco, I know we should be able to readin AMBER's mdcrd files, did I do anything wrong here?  Could you mind to let me if I still did anything wrong here?
>
>
> Best regards,
>
>
> Catherine
>
>
>
>
> Hi Catherine,
> you should install any gromacs *4.5.x*, and then you can use gromacs
> with each trajectory supported by VMD because gromacs is able to use VMD plugin
> to
> perform trajectory reading.
> Basically:
> 1) Install the latest gromacs version
> 2) Install VMD
> 3) Set the variable VMD_PLUGIN_PATH to contain the complete path of the
> molfile vmd directory.
>    In my case, for example:  VMD_PLUGIN_PATH=/apps/vmd/1.9/**lib/vmd
> /plugins/LINUXAMD64/**molfile
>
> Francesco
>
>


-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120403/e7b142df/attachment.html>