Hi,<br>Read the error information carefully. Probably you are trying to read a amber trajectory. Try installing vmd and set the VMD_PLUGIN_PATH variable to the plugin directory inside vmd installation. Gromacs can then read the trajectory using the vmd plugin. <br>
<br><div class="gmail_quote">On Sat, May 26, 2012 at 6:42 PM, a a <span dir="ltr"><<a href="mailto:patd_2@hotmail.com" target="_blank">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">
<div><div dir="ltr">
Dear Sir/Madam,<br><br>I am trying to do the following analysis with GROMACS:<br><br>/usr/local/gromacs/bin/g_covar -s my.pdb -f my.netcdf -o -v<br><br>However, I found the following error message:<br><br>---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br>
GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins.<br>This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD.<br><br>VMD_PLUGIN_PATH not set. Using default location:<br>
/usr/local/lib/vmd/plugins/*/molfile<br><br>Could not open any VMD library.<br>Last error:<br>/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/xyzplugin.so: wrong ELF class: ELFCLASS64<br><br>-------------------------------------------------------<br>
Program g_covar, VERSION 4.5.5<br>Source code file: trxio.c, line: 870<br><br>Fatal error:<br>Not
supported in read_first_frame: D1_md7to23.netcdf<br>For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br><br>However, when I double check my /usr/local/lib/vmd/plugins/LINUXAMD64/molfile directory, I can see netcdfplugin.so file.<br>
<br>Why
the file cannot recognize to use netcdfplugin.so file to read my.netcdf
file, but instead trying to use the xyzplugin.so file?<br><br>I have also set the following path in .bashrc file already.<br>VMD_PLUGIN_PATH=/mydirectory/vmd/lib/vmd/plugins/LINUX/**molfile<br><br>Did I do anything wrong?<br>
<br>Best regards,<br><br>Catherine </div></div>
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