Re: [AMBER] Question about Empirical Valence Bond(EVB) simulation

From: Huang Jing <>
Date: Wed, 4 Jan 2017 06:48:27 +0200

Here shows the example of empirical valence bond calculation by amber;


On Wed, Jan 4, 2017 at 4:21 AM, 没关系 <> wrote:

> Dear Amber users,
> 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?
> Thanks in advance for any help!
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Received on Tue Jan 03 2017 - 21:00:02 PST
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