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_ied/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
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