Hello,
Without knowing specifics about your system, I would guess that ignoring
the contribution of Mg2+ to chelating ADP would be bad in general, and also
not representative of the system you want to simulate.
Mg2+ is parameterized in Amber, you can check the Amber manual, page 51 to
read more about the ion parameters available.
Good luck!
-Christina
On Tue, Feb 19, 2019 at 1:57 PM Antonio Amber Carlesso <
antonio.amber.carlesso.gmail.com> wrote:
> Hi all,
>
> We are interested in performing a MD simulations of a protein where on its
> kinase active is co-crystallized ADP and Mg2+
>
>
>
> Is there any general rule when we would like to simulate a system with a
> divalent cation (in this case Mg2+) in its pocket site?
>
>
> A simplistic approach could be remove the ion before simulations.
>
> When this "simplistic approach" could be considered a bias in the analysis?
>
> Any considerations/reflections about it?
>
>
>
> Thank you!
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST
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Received on Thu Feb 21 2019 - 07:30:02 PST
