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

From: 没关系 <yangzhilin0723.qq.com>
Date: Wed, 4 Jan 2017 14:55:31 +0800

thank you for your help. I have already read the example before,but it only shows an EVB system of two molecules. I want to do an EVB simulation with the protein structure acting as the MD environment. It means reacting molecules considered as the QM region,while the protein acting as the MM region. As i do not find any help from the AMBER manual, i still don't know whether AMBER can do this.


yangzhilin




------------------ 原始邮件 ------------------
发件人: "Huang Jing";<jing.huang8911.gmail.com>;
发送时间: 2017年1月4日(星期三) 中午12:48
收件人: "AMBER Mailing List"<amber.ambermd.org>;

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



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!
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Jan 03 2017 - 23:00:03 PST
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