[gmx-users] adding new ion within the oplsaa force field

[Jose Borreguero]

yes, the ions I have can be considered as bound. I found out I also had to
declare the type of residue as "Ion" in file residues.dat :)

On Fri, Jun 23, 2017 at 4:44 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/23/17 3:50 PM, Jose Borreguero wrote:
>
>> Dear Gromacs users,
>>
>> I'm trying to add a new type of atom as an ion. Looking at already
>> existing
>> ions, such as sodium (NA), I see there's an entry both in files ions.itp
>> and aminoacids.rtp. My question is, what is the rationale of declaring
>> ions
>> both as ions and as residues? Is this always required?
>>
>>
> If you want to process it with pdb2gmx, you need an entry in an .rtp
> file.  If you just have an ion that you're going to add into a box, you can
> rely on ions.itp.  The current implementation covers both cases.  Some
> structures have bound ions and it makes life easier to be able to process
> them with pdb2gmx.
>
> -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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