[gmx-users] Protein-Ligand MS simulation

Justin Lemkul jalemkul at vt.edu
Mon Mar 24 14:22:21 CET 2014

On 3/24/14, 8:52 AM, MUSYOKA THOMMAS wrote:
> Hello. I have a protein pdb and the best pose of a ligand obtained through
> docking using auto dock. However, when I combine the ligand and protein
> using the discovery studio, some residues like Lysine in the protein pdb
> gets protonated as well as the N-terminal residue. Is this unusual and can
> it affect the MD end results?

I can't speak to what's "usual" in Discovery Studio (and there's probably a 
better forum for that, anyway), but it seems like it's just assuming "standard" 
(pH 7) protonation states.  Both lysine and the N-terminus are predominantly 
protonated at neutral pH.  Protonation state can have a major impact on the 
outcome of a simulation, especially in binding sites, and should be chosen wisely.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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