2015-04-14 14:54 GMT-03:00 Justin Lemkul <jalem...@vt.edu>: > > > On 4/14/15 1:48 PM, Marcelo Depólo wrote: > >> 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? >> >> > 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?
> -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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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. -- 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.