Hu Paul,
it is possible the dl library (containing the function to dinamically loading libraries) is missed.
To confirm this hypotesis, try:
ldd path_g_rmsf

On my PC this is the output:

        linux-vdso.so.1 =>  (0x00007fffdddd6000)
libgmxana.so.6 => /apps/gromacs/4.5.5/gnu/lib/libgmxana.so.6 (0x00007f6e50994000) libmd.so.6 => /apps/gromacs/4.5.5/gnu/lib/libmd.so.6 (0x00007f6e50529000)
        libxml2.so.2 => /usr/lib/libxml2.so.2 (0x00007f6e501a9000)
libgmx.so.6 => /apps/gromacs/4.5.5/gnu/lib/libgmx.so.6 (0x00007f6e4fbe6000) * libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f6e4f9e2000)* libnsl.so.1 => /lib/x86_64-linux-gnu/libnsl.so.1 (0x00007f6e4f7c7000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f6e4f542000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f6e4f324000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f6e4ef8f000)
        libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f6e4ed77000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f6e50de2000)

If you miss this library, try to instrall again gromacs including this library

Francesco

Il 07/02/2012 20:04, Kunze, Micha ha scritto:
Hey Paul,

cant help you with the plugin issue, but have you instead tried loading the dcd trajectory into vmd and save it as trr?

Cheers,
Micha

On 7 Feb 2012, at 18:18, "PAUL NEWMAN" <paulcliz...@gmail.com <mailto:paulcliz...@gmail.com>> wrote:

Dear Gromacs users,

This is my second email since I tried the previous advises and did NOT work.

I want to use the Gromacs analysis tools for analyzing Namd output files (*.dcd files) I installed Gromacs 4.5.4 (64 bits) and it works well. In addition I installed VMD 1.9 (64 bits) 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*


Can anyone tell me if Gromacs really works with the VMD pulgin?

I will highly appreciate to know it so I can start looking for another alternatives.

Thanks so much



--
Cheers,

Paul


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