[gmx-users] Position restraint for ions

[Marcelo Depólo]

2015-04-14 17:26 GMT-03:00 Justin Lemkul <jalemkul at 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
>
> 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)