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(?).
Best,
Qiantao
On Fri, Apr 20, 2012 at 3:07 AM, Fernando Martín García <fmgarcia.cbm.uam.es
> 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"
> C/ NICOLáS CABRERA, 5.
> UAM University. Cantoblanco, 28049 Madrid. Spain.
> TEL: (+34) 91-196-4662 FAX: (+34) 91-196-4420
> Web: http://fertoledo.wordpress.com/
> ==============================================
>
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Received on Fri Apr 20 2012 - 11:00:03 PDT
