Here shows the example of empirical valence bond calculation by amber;
http://ambermd.org/evb_pmf.html
jing
On Wed, Jan 4, 2017 at 4:21 AM, 没关系 <yangzhilin0723.qq.com> 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
