Hi, 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.
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. Roland On Fri, Mar 30, 2012 at 11:47 PM, a a <[email protected]> wrote: > Dear Sir/Madam, > > > I am trying to run covar using mdcrd file. > > > I installed the vmd and gromacs 4.5.5. to my computer. I also set the > VMD_PLUGIN_PATH by adding a line in .bashrc file in my home directory. > > > VMD_PLUGIN_PATH=/home/cmche/AnnieSoftwares/vmd_ie > d/lib/vmd/plugins/LINUX/molfile > > > When I did the following command: > > /usr/local/gromacs/bin/g_covar_d -s average.pdb -f md0.mdcrd -o -v > > > I get the following error message. > > > ------------------------------------------------------- > 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 > ------------------------------------------------------- > > > Thanks to Francesco, 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? > > > Best regards, > > > Catherine > > > > > 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 > > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
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