AMBER Archive (2007)

Subject: Re: AMBER: QM/MM in reaction pathways?

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Tue Aug 28 2007 - 09:55:20 CDT

On 8/28/07, Qiang Zhong <zqiang320_at_webmail.hzau.edu.cn> wrote:
> Dear Amber users:
> I am calculating free energy of reaction of protein. I need some
> tutorial or document about this field.I have study tutorial "A Coupled
> Potential QM/MM Simulation". but I don't think it suit to me. Could somebody
> tell me some tutorial or document about this?

To do this, you probably want something like umbrella sampling or
steered molecular dynamics. I don't think we have a tutorial for that,
but you can look in sections 6.7 and 6.8 in the manual. When you get
an idea of how to do that, then you can apply the ideas in the
tutorial you cited to use QM. (It should be just a keyword change, and
indicated in the tutorial.)

Gustavo.
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