Use gmxcheck to find out what's in the files. Think about how you used xtcgroups. Consider using tpbconv to make a matching subset from your .tpr.
Mark On Wed, May 22, 2013 at 11:53 AM, Arunima Shilpi <writetoas...@gmail.com>wrote: > Respected sir > > I want to calculate the distance between protein and ligand after I have > run the production step. I used the following command.. > > g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n index.ndx > > Groups I selected was > Group 1 (protein) > Group 13 (ligand) > > It says the following error > > Molecule in topology has atom numbers below and above natoms (11793). > You are probably trying to use a trajectory which does not match the first > 11793 atoms of the run input file. > > how to debug the error... > > -- > > Thanking You with Regards. > > Arunima Shilpi > > Ph. D Research Scholar(Cancer & Epigenetics) > Department of Life Science > National Institute of Technology > Rourkela > Odisha > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
