Re: [AMBER] a question on molecular dynamics simulation

From: David A Case <>
Date: Fri, 6 Mar 2015 10:09:44 -0500

On Fri, Mar 06, 2015, Brett wrote:
> 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.
> 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?

Amber has only extremely rudimentary support for "active site" simulations.
You might see if there is some way you can naturally truncate your system
(i.e. as one might do experimentally).

Are you sure that you cannot afford to simulate the full complex?


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Received on Fri Mar 06 2015 - 07:30:03 PST
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