[gmx-users] All atom MD Simulation

[Ullmann, Thomas]

>> Can we analyse catalytic mechanism of an enzyme using the classical all
>> atom MD simulation.
>
>No.

I would say, that is a bit too pessimistic and unnecessarily demotivating. You can not directly simulate the catalytic reaction without employing  a quantum chemical treatment (or a reactive force field) for the catalytic site and the reacting compounds, but even without that, just with classical MD, you can still learn a lot about the enzymatic mechanism, e.g., about the binding of a substrate, the stabilization of reaction intermediates with respect to educt(s) and product(s)  in the catalytic site relative to the same reaction in solution, the release of a product(s) etc. A literature research will turn up innumerable examples.

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R. Thomas Ullmann, PhD
Theoretical & Computational Biophysics
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11
37077 Göttingen, Germany
thomas.ullmann at mpibpc.mpg.de
www.bisb.uni-bayreuth.de/People/ullmannt
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________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: Wednesday, September 03, 2014 1:42 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] All atom MD Simulation

On 9/3/14, 7:40 AM, Anitha wrote:
> Can we analyse catalytic mechanism of an enzyme using the classical all
> atom MD simulation.
>

No.

-Justin

--
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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