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Hu Paul, <br>
it is possible the dl library (containing the function to
dinamically loading libraries) is missed.<br>
To confirm this hypotesis, try:<br>
ldd path_g_rmsf<br>
<br>
On my PC this is the output:<br>
<br>
linux-vdso.so.1 => (0x00007fffdddd6000)<br>
libgmxana.so.6 =>
/apps/gromacs/4.5.5/gnu/lib/libgmxana.so.6 (0x00007f6e50994000)<br>
libmd.so.6 => /apps/gromacs/4.5.5/gnu/lib/libmd.so.6
(0x00007f6e50529000)<br>
libxml2.so.2 => /usr/lib/libxml2.so.2
(0x00007f6e501a9000)<br>
libgmx.so.6 => /apps/gromacs/4.5.5/gnu/lib/libgmx.so.6
(0x00007f6e4fbe6000)<br>
<b> libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2
(0x00007f6e4f9e2000)</b><br>
libnsl.so.1 => /lib/x86_64-linux-gnu/libnsl.so.1
(0x00007f6e4f7c7000)<br>
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6
(0x00007f6e4f542000)<br>
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
(0x00007f6e4f324000)<br>
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6
(0x00007f6e4ef8f000)<br>
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1
(0x00007f6e4ed77000)<br>
/lib64/ld-linux-x86-64.so.2 (0x00007f6e50de2000)<br>
<br>
If you miss this library, try to instrall again gromacs including
this library<br>
<br>
Francesco<br>
<br>
Il 07/02/2012 20:04, Kunze, Micha ha scritto:
<blockquote
cite="mid:887D918F-AFDB-4C32-B194-B8DBD6ADE861@ucl.ac.uk"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<div>Hey Paul,</div>
<div><br>
</div>
<div>cant help you with the plugin issue, but <span
class="Apple-style-span" style="-webkit-tap-highlight-color:
rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color:
rgba(175, 192, 227, 0.230469);
-webkit-composition-frame-color: rgba(77, 128, 180, 0.230469);
">have you instead tried loading the dcd trajectory into vmd
and save it as trr? </span></div>
<div><br>
Cheers,</div>
<div>Micha</div>
<div><br>
On 7 Feb 2012, at 18:18, "PAUL NEWMAN" <<a
moz-do-not-send="true" href="mailto:paulclizana@gmail.com">paulclizana@gmail.com</a>>
wrote:<br>
<br>
</div>
<blockquote type="cite">
<div>Dear Gromacs users,<br>
<br>
This is my second email since I tried the previous advises and
did NOT work. <br>
<br>
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 ) <br>
<div id=":1al"><br>
I verified that VMD_PLUGIN_PATH is pointing out to the right
folder. However when I run for example
<br>
<br>
<b>g_rmsf_d -f file.dcd -s file.pdb </b> <br>
<br>
I got the following error<br>
<br>
<b>The file format of file.dcd is not a known trajectory
format to GROMACS. Please make sure that the file is a
trajectory!<br>
<br>
GROMACS will now assume it to be a trajectory and will try
to open it using the VMD plug-ins.</b>
<b><br>
This will only work in case the VMD plugins are found and
it is a trajectory format supported by VMD.<br>
<br>
No plugin for dcd found</b><br>
<br>
<br>
Can anyone tell me if Gromacs really works with the VMD
pulgin? <br>
<br>
I will highly appreciate to know it so I can start looking
for another alternatives.<br>
<br>
Thanks so much<br>
<br>
<div class="yj6qo ajU">
<div id=":1bd" class="ajR" tabindex="0"><img
moz-do-not-send="true" class="ajT"
src="cid:images/cleardot.gif"></div>
</div>
</div>
<br clear="all">
<br>
-- <br>
Cheers, <br>
<br>
Paul<br>
<br>
<br>
</div>
</blockquote>
<blockquote type="cite">
<div><span>-- </span><br>
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Use the </span><br>
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</blockquote>
<br>
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