[gmx-users] modelling of calcium ions

[Justin Lemkul]

On 2/5/17 4:18 AM, Mahboobeh Eslami wrote:
> Hi all GMX usersI hope you are wellI want to simulate a protein-ligand complex. There are two calcium ions in the crystallographic structure of protein. I want to keep them. I find non-bonded parameters of Ca+2. How can I use these parameter for modelling of calcium ions.? Please guide me.ThanksBest
>

Ca2+ is already present in every force field in GROMACS.  pdb2gmx should handle 
it out of the box as long as the residue is named appropriately.  If you have 
(good) reason to change any aspects of the parameters, you'll have to alter 
ffnonbonded.itp to change the attributes of the corresponding atom type.

-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

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