AMBER Archive (2009)

Subject: Re: [AMBER] Can bond clevage & formation conducted by qm/mm via sander?

From: Mahmoud A. A. Ibrahim (m.ibrahim1982_at_yahoo.com)
Date: Tue May 05 2009 - 12:15:18 CDT

Dear Dr. Gustavo Seabra

Me too a bigenner in this fieldI am a bit confused. According to your
reply, you say Bond can be broken and formed during QM/MM, don't you?

I think it can be happened if the bond only falls in QM region, i.e
there is no bond formation or clevage in MM even if you run for ver
long time. Am I right?

I took forward to hearing from you.

Thanks in Advance;

M. Ibrahim

--- On Tue, 5/5/09, Gustavo Seabra <gustavo.seabra_at_gmail.com> wrote:

From: Gustavo Seabra <gustavo.seabra_at_gmail.com>
Subject: Re: [AMBER] Can bond clevage & formation conducted by qm/mm via sander?
To: "AMBER Mailing List" <amber_at_ambermd.org>
Date: Tuesday, May 5, 2009, 6:04 PM

> However, there's no change for proton transfer (ie, GLH --> GLU & proton
> transfer to ligand) by monitoring the corresponding distance variation,
> and it remained stable.
>
> I'm wondering if such thought is reasonable? Could anyone provide me
> with some suggestion or reference?

Why would you expect the proton to be transfered? I don't see in your
input file anything to drive that change. If you are just running a
long MD and expecting to see it happen naturally, be aware that it may
take a *very* long time for it to happen... (if it does at all).

Gustavo.

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