Re: [AMBER] Reaction profile calculation in Amber by QM/MM method

From: Jason Swails <>
Date: Tue, 02 Sep 2014 09:00:27 -0400

On Tue, 2014-09-02 at 12:54 +0530, MOHD HOMAIDUR RAHMAN wrote:
> Dear Amber user
> There is any tutorials available for study of reaction energy profile for
> enzymatic catalyze reaction in Amber through QM/MM module.

What are you trying to do? "Reaction energy profile" is fairly
ambiguous. Are you looking for a relaxed potential energy profile (one
that you get by minimizing the structure at various points along a
reaction coordinate)? Are you looking for a free energy profile (also
called a potential of mean force, or PMF) that accounts for the entropic
effects of the system dynamics? These are different, and are computed
differently. The former is far faster to compute, while the latter
provides a more clear-cut comparison with experiment.

The former can be accomplished by figuring out how to assign geometric
restraints to your reaction coordinate (see the NMR restraint syntax in
chapter 23 of the Amber 14 manual for details), and then simply perform
a (thorough) minimization.

The latter can be accomplished with methods such as umbrella sampling or
steered molecular dynamics. There are tutorials for both of these on
the tutorial website (advanced tutorial A10 and advanced tutorial A17).
Tutorial A10 actually walks through setting up a steered MD simulation
to model a proton transfer using QM/MM (although it uses the NCSU module
rather than the NMR restraints which are better supported). Tutorial
A17 shows you how to construct a PMF using umbrella sampling with a pure
MM potential, but the umbrella sampling part is orthogonal to whether
you use a pure force field or QM/MM.

I would suggest looking through those tutorials, consulting the manual,
and experimenting with different options until you get a basic idea of
what works for your system. Once you have the recipe down and the
details worked out, then you should invest the time and resources into
carrying out production-level simulations.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Sep 02 2014 - 06:00:02 PDT
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