[gmx-users] Position restraint for ions

Marcelo Depólo marcelodepolo at gmail.com
Tue Apr 14 21:26:01 CEST 2015

> *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)

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