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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