Hi!
I was wondering if there is any clear way to create position restraints for ions. I am using: *g_select -s rna_ions.gro -n index.ndx -on rna_ion.ndx -select 'group "non-Water"'* -> to create an index for my RNA and Ions; and: *genrestr -f rna_ions.gro -n rna_ion.ndx -o rna_ion.itp -fc 800 800 800* -> to create an .itp file for them. I am also including this new .itp file to the topology using the proper 'ifdef' statements, but I get this when I run grompp: *Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in position_restraints out of bounds (1-1748).This probably means that you have inserted topology section "position_restraints"in a part belonging to a different molecule than you intended to.In that case move the "position_restraints" section to the right molecule.* It seems the ions are not included as the same moleculetype as the RNA and Gromacs see this as an error. Would someone knows a neat way to do this? Cheers! -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.