Re: [AMBER] Catalysis mechanism of ATPase

From: Pratul Agarwal <>
Date: Mon, 20 May 2019 22:59:27 +0000

If you haven't already received replies, may be this will be of some help.

As you said, regular MD simulations can only model fixed electronic states, therefore, are not suitable for investigating enzyme mechanisms (such as ATPases). There are several methods described in the AMBER manual (EVB method for example) when combined with classical MD can and have been used to investigate enzyme mechanisms. It depends on what you are trying to investigate, but QM/MM method appears to be the rational choice for looking at ATPase catalytic mechanism. The issue of time-scale depends on the method (and level of quantum theory) you use to model the reaction pathway.

AMBER's QM/MM functionality is implemented in sander, which is not available on GPUs. So to the best on my knowledge, QM/MM modeling won't benefit from GPUs. Others on the list can correct me. Also based on our labs experience, a lot more computing power than just a work station is required to obtain sufficient sampling to represent pathways of enzyme reactions.

If you really want to use AMBER on GPUs, you can perform MD on selected states (reactant, product and intermediate(s)).

Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)

On 5/19/2019 7:29 AM, sunyeping wrote:

Dear all,

I wish to investigate the catalysis mechanism of ATPase which hydrolyze ATP into ADP and pi. Can the bond breaking process simulated by molecular dynamcis simulation with amber? I know MM/QM may do this, but what will the time scale be? Is it feasible in a usual workstation with GPU?

Best regards.
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Received on Mon May 20 2019 - 16:00:02 PDT
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