On Fri, Aug 12, 2011, Maura Catherine Mooney wrote:
>
> Now, I wonder would it be scientifically valid to model the
> divalent metal and 4 coordinating waters using QM and model the NTP
> with the classical MM, using Bryces parameters?
Divalent ions are notoriously difficult to model, and I think you will have to
search the literature, and do some small molecule calculations yourself, to
answer your question. It makes a big difference whether you expect the first
coordination shell to the ion to change during the course of the simulation.
Also, it's pretty odd to have some of the first coordination shell ligands be
QM entities, and others be MM.
My personal view: if you have a "structural" whose local environment is
constant, then you are likely to get reasonable results with models that keep
the first shell ligands always bound. (Note that "reasonable" does not imply
quantitatively accurate energetics.) If you expect to have first shell
ligands exchanging, you need to plan to put in lots of work in
parameterization.
Put another way: there is a reason why there are no standard "Amber"
parameters for ions like Mg2+.
...mainly by $.02.....dac
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Received on Fri Aug 12 2011 - 07:00:02 PDT
