[gmx-users] Position restraint for ions

[Marcelo Depólo]

2015-04-14 14:54 GMT-03:00 Justin Lemkul <jalemkul at 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
Marcelo Depólo Polêto
Student of MSc Cell and Molecular Biology - UFRGS (Brazil)
B.Sc. Biochemistry - University of Viçosa (Brazil)