Re: [AMBER] a question on molecular dynamics simulation

From: Jason Swails <>
Date: Fri, 6 Mar 2015 10:03:48 -0500

On Fri, Mar 6, 2015 at 8:14 AM, Brett <> wrote:

> Dear All,
> Suppose I have a very large protein-complex, and I want to do the
> molecular dynamics simulation of its activation center. If I do the
> molecular dynamics simulation of the whole, it will cost a lot of
> calculation. Suppose I only focus on the activation center, I am afraid in
> fact the part outsides of the activation center has relation with the
> dynamics simulation of the activation center.

​It stands to reason that if only the active site was important to enzyme
function, and the rest of the system was superfluous, that evolution would
have trimmed away the rest (or at least a large amount of it).

The rest of your protein is very likely to be critical to the proper
functioning of the enzyme. Either by stabilizing the native fold that puts
the active site in the correct geometry, by increasing the substrate
discrimination by structural or electrostatic topology, allosteric effects,

Can you please introduce me the compromising method which take a look on
> the whole protein compplex but focus on the activation cnter? Can you
> introduce a tutorial on it to me?

​I've seen some methods for truncating a system when trying to analyze it
*after* an MD simulation (e.g., ​
​), but never one in which the system itself is truncated around the active

If your system is too large to simulate, you are probably better off
looking for a more approximate model (like any of a number of coarse grain
models) rather than trying to snip away "irrelevant" parts of the protein.
Because when you think about it, the only way you'd be able to *justify*
snipping away parts of the protein is by showing that doing so doesn't
affect your results. And to do that, you need to run the simulation of the
full system as your control, anyway...


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Mar 06 2015 - 07:30:02 PST
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