Vlad,
it really depends what you want from your simulation.
To follow dynamics, your combination of parameters seems reasonable. You
will just have to deal with the well known stickiness of Mg++ to charged
phosphates.
For more advanced problems (binding energies, protonation states, etc.)
things are much more complicated. For example, you ignore polarization
and the fact that the LJ pairwise MM parameters of poly-phosphates and
Mg++ have not been tuned to reproduce geometries, energies, etc of
complexes.
all the best,
George
On 08/27/2012 04:21 AM, Vlad Cojocaru wrote:
> Dear Amber users,
>
> I am looking into starting simulations of a protein that has a GDP and a
> MG ion in the active site.
> I know that in the database of AMBER parameters there are the Carlson
> parameters for GDP and the new Sorensen parameters for MG.
>
> I also found this comment from David Case which made me wonder about
> GDP. Is there anything new on the paper mentioned there ?
> http://archive.ambermd.org/201112/0208.html
>
> I also read carefully this thread.
> http://archive.ambermd.org/201205/0530.html
>
> Before starting simulations, I would be very grateful if people that
> have been using these parameter sets would comment on their experience
> with them (besides what is published in the respective references).
>
> If people are aware of other parameter sets, not available in the data
> base but worth trying out, I would also be very interested.
>
> Best wishes
> Vlad
>
>
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Received on Mon Aug 27 2012 - 10:00:02 PDT
