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

[Justin Lemkul]

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

==================================================