Re: [AMBER] QM/MM and water box type

From: Qiantao Wang <>
Date: Fri, 20 Apr 2012 12:59:33 -0500

Hi Fernando,

Just wandering what QM model did you use? If you were using semi-empirical
NDDO-based models, the problem you see could just because of the arg-glu
(QM-QM) interaction cannot compete with the arg/glu-water (QM-MM)
interaction, as some semi-empirical model well under-estimates the hydrogen
bonding. I would first try different QM model and QM/MM coupling methods
first to see if it helps rather than different water models, considering
you have been using TIP3P water in your previous calculations(?).


On Fri, Apr 20, 2012 at 3:07 AM, Fernando Martín García <
> wrote:

> Dear Amber users,
> I've been simulating a reaction with QM/MM method. In my catalytic
> reaction center I have i salt bridge exposed to the media and that close
> it. During 20 ns, that bridge is stable, but when I introduce it QM
> calculation it starts to be unstable. Revising the structure, I see it
> interacts with solvent water. These waters are a TIP3 box and I have one
> question: could it be a problem between TIP3 and QM region because their
> high diffusion coefficient, and so, it could try to broke my bridge
> (between an arginine and glutamic)? What kind of water would be better
> to use?.
> Thank you,
> --
> ==============================================
> Fernando Martín García
> Molecular Modelling Group - Lab 312.1
> Molecular Biology Center "Severo Ochoa"
> UAM University. Cantoblanco, 28049 Madrid. Spain.
> TEL: (+34) 91-196-4662 FAX: (+34) 91-196-4420
> Web:
> ==============================================
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Received on Fri Apr 20 2012 - 11:00:03 PDT
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