[gmx-users] Protein preparation

[Justin Lemkul]

On 3/26/17 9:44 AM, Quin K wrote:
> Hi
>
> I'm new to Gromacs.
> I have a question regarding protein preparation for MD simulation.
>
> I ran a 50 ns MD simulation but later found out that the protein has a
> charge.
> I found that there is a Mg2+ Ion in the protein crystal structure. Should I
> remove this Mg2+ ion from protein before addition of ions to the protein ??
>
> Following is the protein I used.
>
> http://www.rcsb.org/pdb/explore.do?structureId=3a5j
>

If the ion is catalytically or structurally significant it should be retained. 
If it's a consequence of some crystallization medium and may not be relevant in 
solution or for whatever your purposes are, then it can be removed.  But that's 
your homework to do based on your understanding of the biology and the goals of 
your work.

-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

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