AMBER Archive (2009)

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

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Tue May 05 2009 - 12:04:37 CDT

> 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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