Re: [AMBER] QM/MM calculation in Amber

From: David A Case <>
Date: Sun, 6 Aug 2017 14:37:38 -0400

On Sat, Aug 05, 2017, Albert wrote:
> I would like to perform QM/MM calculation for the energy of an enzyme
> transitional stage. I have seen there is a simple QM/MM tutorial in the
> Amber webpage, however it has nothing to do with how to scan the
> transitional stage. So I am just wondering is there any other more
> detailed tutorial showing how to scan enzyme catalytic transitional stage?

You can look at the umbrella sampling or nudged elastic band tutorials, or
the non-equilibrium free energy tutorial Basically, sampling of configuration
space is mostly orthogonal to whether or not you use QM/MM as a Hamiltonian.
(Of course, the sorts of reaction coordinates that you want if you your making
and breaking bonds are generally different -- more localized -- than for
other sorts of conformational changes.)


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Received on Sun Aug 06 2017 - 12:00:04 PDT
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