[gmx-users] Deprotonated Asp and Glu

[Justin Lemkul]

On 5/24/16 8:30 AM, sun wrote:
> Hello I have simulated a protein ligand complex and analyzed the trajectory.
> After visualization of time frames and clusters.pdb; It occurs to me that the
> Asp and Glu are nit deprotonated although during pdb2gmx I used -inter
> command and deprotonated both residue according to pH 7. Can anyone tell me
> if this possible during visualization? or what might the problem be? My

The simulation won't do anything you don't tell it.  Asp and Glu are 
deprotonated by default in pdb2gmx, so there should be no need to do anything to 
them.  Probably you made the wrong choice when setting up the topology.  The 
contents of the topology are definitive; if you're seeing unexpected "bonds" in 
a visualization software, those are typically guessed from the coordinates and 
are not necessarily real (e.g. nearby water/ligand H might get "bonded" to an 
Asp/Glu).

-Justin

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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

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