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<pre style="background-color: rgb(255, 255, 255); font-size: medium; ">Dear Sir/Madam,</pre><pre style="background-color: rgb(255, 255, 255); font-size: medium; "><br></pre><pre style="background-color: rgb(255, 255, 255); font-size: medium; ">I am trying to run covar using mdcrd file.</pre><pre style="background-color: rgb(255, 255, 255); font-size: medium; "><span style="font-family: Tahoma; "><br></span></pre><pre style="background-color: rgb(255, 255, 255); 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="background-color: rgb(255, 255, 255); "><font face="Tahoma" size="3"><br></font></pre><pre style="background-color: rgb(255, 255, 255); "><font face="Tahoma" size="3">VMD_PLUGIN_PATH=/home/cmche/AnnieSoftwares/vmd_ie
d/lib/vmd/plugins/LINUX/molfile</font></pre><pre style="background-color: rgb(255, 255, 255); "><font face="Tahoma" size="3"><br></font></pre><pre style="background-color: rgb(255, 255, 255); "><font face="Tahoma" size="3">When I did the following command: </font></pre><pre style="background-color: rgb(255, 255, 255); "><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="background-color: rgb(255, 255, 255); font-size: medium; ">I get the following error message.</pre><pre style="background-color: rgb(255, 255, 255); font-size: medium; "><br></pre><pre style="background-color: rgb(255, 255, 255); "><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 http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------</font><span style="font-size: 12pt; ">
</span></pre><div><br></div><pre style="background-color: rgb(255, 255, 255); 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="background-color: rgb(255, 255, 255); font-size: medium; "><br></pre><pre style="background-color: rgb(255, 255, 255); font-size: medium; ">Best regards,</pre><pre style="background-color: rgb(255, 255, 255); font-size: medium; "><br></pre><pre style="background-color: rgb(255, 255, 255); font-size: medium; ">Catherine</pre><pre style="background-color: rgb(255, 255, 255); font-size: medium; "><br></pre><pre style="background-color: rgb(255, 255, 255); font-size: medium; "><br></pre><pre style="background-color: rgb(255, 255, 255); font-size: medium; "><br></pre><pre style="background-color: rgb(255, 255, 2
55); font-size: medium; ">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> </div></body>
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