Hi, Allow me to be the first to archive a message with "negative index".
I ask for an index file: make_ndx_s -f ???.pdb -o ???.ndx and specify: a AG to select all the silver atoms into a group. The index file then clearly numbers and lists the atoms: all in [ system ], again all atom numbers in empty brackets [ ] and then my silver atoms in the [ AG ] group. I proceed to define a box: editconf_s -f ???.pdb -n ???.ndx -o ???.gro -bt cubic The output gives: ... Select a group for output: WARNING: negative index -1 in group System WARNING: negative index -1 in group System Group 0 ( System) has 68 elements Group 1 ( AG) has 13 elements Select a group: 0 Selected 0: 'System' Segmentation fault Perplexing. I found Travis Trudeau's message about having a zero index and tried finding atom numbering: grompp_s -f ???.mdp -c ???.pdb -p ???.top -o ???.tpr -n ???.ndx But again got: ... initialising group options... processing index file... WARNING: negative index -1 in group System WARNING: negative index -1 in group System Making dummy/rest group for T-Coupling containing 33 elements ... So, if anyone could shed some light on how to overcome the negative index hurdle it would be much appreciated, Chris Rowan University of Victoria _______________________________________________ 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/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/mailing_lists/users.php
