See my previous response. You don't need a .tpr for trjconv (unless you are doing pbc operations). trjconv -h will also tell you that. Just use trjconv -s my.pdb
Chris. -- original message -- Sorry for my ignorance, since the help manual uses tpr file for the first two steps before running g_spatial, could you please tell me how I should do them without tpr. Also when I just run g_spatial (without the first two steps) I get the distribution of all the anions around cations, so it is not informative. Thank you so much for all the help -- 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
