On Wed, Jan 04, 2017, 没关系 wrote:
>
> I want to do an EVB simulation of the hydrogen transfer step of an
> enzymatic reaction. With help of the Amber Manual,I have successfully
> ran an EVB simulation including two molecules and obtained a PMF curve.
> However, I do not know how to do an EVB simulation including the whole
> protein environment（the two molecules in the active center are used
> in EVB calculation, and the protein acts as the environment in the MD
> simulation）. Does Amber can do so ? if it can do, how to identify the
> EVB region and the protein environment？
Yes. You define two potentials and a mixing term. The "environment" parts
are the same in V1 and V2. You don't have to explicitly say what is the
environment and what is not.
...dac
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Received on Thu Jan 05 2017 - 18:30:02 PST
