2015-04-14 17:26 GMT-03:00 Justin Lemkul <jalem...@vt.edu> > > > On 4/14/15 3:25 PM, Marcelo Depólo wrote: > >> *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? >> >> > I can offer no rationalization without seeing your commands and perhaps > getting access to your files. Merging RNA+ions is something I do > routinely, but I always do that before adding any water or anything else. >
So how do you insert your ions without water to be exchanged for the ions? -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.
