[gmx-users] Position restraint for ions

Justin Lemkul jalemkul at vt.edu
Tue Apr 14 22:53:14 CEST 2015

On 4/14/15 4:50 PM, Marcelo Depólo wrote:
> 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?

I don't restraint bulk ions.  I'm only interested in structurally bound ions, 
and there are various reasons to restrain those during different processes.  Why 
do you want to restrain bulk ions?

You should be able to do whatever you like, but without more information I can't 
diagnose what's happening in your case.



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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