[gmx-users] modelling of calcium ions
jalemkul at vt.edu
Sun Feb 5 17:18:21 CET 2017
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 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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