AMBER Archive (2006)

Subject: Re: AMBER: question about QM/MM in amber9

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Thu May 25 2006 - 05:57:25 CDT

aixiaoli wrote:
> Dear Amber users:
> I have a question about the QM/MM module in Amber9, I don't know if QM/MM can define the QM center dynamically, did not find it in manual. For example, for receptor+ligand simulation in Waterbox, first I define ligand and one water near to it as QM center, but later, after running MD for tens or hundreds ps, this water molecule may go far from the ligand and have no interaction with it, while another water come to the ligand, so, is it possible to change QM center dynamically during MD? Based on distance from ligand or some other criteria instead of using residue number?
>
> Thank you very much for any help in advance :)
>
>
>
>
> Yours sincerely,
> aixiao
>
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Aixiao, The simple answer is not, it cannot be done at this moment.Once
you define the QM set, it stays fixed for the duration of that run.
There are a couple of groups working on some type of implementation of
this, but at least ours will not be available until amber 10. 

-- 
                           Dr. Adrian E. Roitberg
                             Associate Professor
              Quantum Theory Project and Department of Chemistry

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
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