[gmx-users] Position restraint for ions

Justin Lemkul jalemkul at vt.edu
Tue Apr 14 19:54:45 CEST 2015

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.



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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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