Hi, 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.
On Sat, May 26, 2012 at 6:42 PM, a a <[email protected]> wrote: > Dear Sir/Madam, > > I am trying to do the following analysis with GROMACS: > > /usr/local/gromacs/bin/g_covar -s my.pdb -f my.netcdf -o -v > > However, I found the following error message: > > > --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > 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. > > VMD_PLUGIN_PATH not set. Using default location: > /usr/local/lib/vmd/plugins/*/molfile > > Could not open any VMD library. > Last error: > /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/xyzplugin.so: wrong ELF > class: ELFCLASS64 > > ------------------------------------------------------- > Program g_covar, VERSION 4.5.5 > Source code file: trxio.c, line: 870 > > Fatal error: > Not supported in read_first_frame: D1_md7to23.netcdf > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > > However, when I double check my > /usr/local/lib/vmd/plugins/LINUXAMD64/molfile directory, I can see > netcdfplugin.so file. > > Why the file cannot recognize to use netcdfplugin.so file to read > my.netcdf file, but instead trying to use the xyzplugin.so file? > > I have also set the following path in .bashrc file already. > VMD_PLUGIN_PATH=/mydirectory/vmd/lib/vmd/plugins/LINUX/**molfile > > Did I do anything wrong? > > Best regards, > > Catherine > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- C. Balasubramanian
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