Hi,<div><br></div><div>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.</div>
<div><br></div><div>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. </div><div><br></div><div>Roland<br><br><div class="gmail_quote">
On Fri, Mar 30, 2012 at 11:47 PM, a a <span dir="ltr"><<a href="mailto:patd_2@hotmail.com">patd_2@hotmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<pre style="font-size:medium">Dear Sir/Madam,</pre>
<pre style="font-size:medium"><br></pre>
<pre style="font-size:medium">I am trying to run covar using mdcrd file.</pre>
<pre style="font-size:medium"><span style="font-family:Tahoma"><br></span></pre>
<pre style="font-size:medium"><span style="font-family:Tahoma">I installed the vmd and gromacs 4.5.5. to my computer. </span><span style="font-family:Tahoma">I also set the </span><span style="font-family:Tahoma">VMD_PLUGIN_PATH by adding a line in .bashrc file in my home directory.</span></pre>
<pre style><font face="Tahoma" size="3"><br></font></pre>
<pre style><font face="Tahoma" size="3">VMD_PLUGIN_PATH=/home/cmche/AnnieSoftwares/vmd_ie
d/lib/vmd/plugins/LINUX/molfile</font></pre>
<pre style><font face="Tahoma" size="3"><br></font></pre>
<pre style><font face="Tahoma" size="3">When I did the following command: </font></pre>
<pre style><span style="font-family:Tahoma;font-size:12pt">/usr/local/gromacs/bin/g_covar_d -s average.pdb -f md0.mdcrd -o -v</span></pre>
<div><span style="font-family:Tahoma"><br>
</span></div>
<pre style="font-size:medium">I get the following error message.</pre>
<pre style="font-size:medium"><br></pre>
<pre style><font size="3">-------------------------------------------------------
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 <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a>
-------------------------------------------------------</font><span style="font-size:12pt">
</span></pre>
<div><br>
</div>
<pre style="font-size:medium">Thanks to <span style="font-family:Tahoma">Francesco, </span><span style="font-family:Tahoma">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?</span></pre>
<pre style="font-size:medium"><br></pre>
<pre style="font-size:medium">Best regards,</pre>
<pre style="font-size:medium"><br></pre>
<pre style="font-size:medium">Catherine</pre>
<pre style="font-size:medium"><br></pre>
<pre style="font-size:medium"><br></pre>
<pre style="font-size:medium"><br></pre>
<pre>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</pre>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br>
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