> *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? >>> >>> >> The ions need to be merged into the RNA [moleculetype] definition in >> order for this to work. This isn't something that is done after the fact >> with index groups as you're trying above; the topologies need to be merged, >> e.g. with pdb2gmx -chainsep -merge, or by hand if the ions aren't part of >> the input coordinate file. >> >> Thanks, Justin. I have tried that by using '-merge all' but this created > a .top without the ions. RNA and water only. grompp even warned me that my > system now has non-zero charge. Any ideas? > And surprisingly, if I remove the water with 'editconf', and only then I merge them using pdb2gmx, then the topology is written right (with the ions and zero net charge). Confusing, han?
> > >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 629 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> >> -- 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.
