Re: [AMBER] the out file of qm/mm in amber

From: Jason Swails <>
Date: Wed, 10 Sep 2014 08:25:14 -0400

On Wed, 2014-09-10 at 20:09 +0800, 王珍 wrote:
> Hi all,
> Recently, I want to optimize the molecule. I use the Amber to
> simulate the atom in MM region, and use the Gaussian to simulate the
> atom in QM region. But there is no MM atoms in the Log file of
> outfile , It just has the atom in QM region.
> Thank you in advance.

Correct. You posted the log of Gaussian, which exclusively handles the
QM part of the calculation. To the QM program (Gaussian in this case),
the MM atoms appear like nothing but point charges whose charge value is
equal to the partial atomic charge in the force field. Look in the log
file where it says "Background charge distribution read from input
stream: Point Charges: ..." -- those are the MM atoms.

Gaussian is capable of QM/MM through its ONIOM functionality, but Amber
makes no use of that so there will never be any MM atoms in QM input
files outside of the simple point-charge distribution.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Sep 10 2014 - 05:30:04 PDT
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