Hi Anu,
> On Jan 29, 2016, at 9:26 AM, anu chandra <anu80125.gmail.com> wrote:
>
> Hello Amber users,
>
> The protein I am working with have a Mn2+ ion at its active site. The ion
> suspected to form coordination bond with neighboring residues and these
> bonds will break and re-form during the course of reaction.
Does any chemical reaction happened during the process? For example, catalysis reaction which produces new compound.
> As read from
> the tutorial page, I suppose I should use the non-bonded model. But, after
> going through the description of bonded and non-bonded models in the
> tutorial page, I am a little confused about the model I should choose. The
> tutorial says about the bonded model that -
>
> ' While ligand exchange of coordination number (CN) switching process
> certainly do happen in protein metal sites, these occur on much slower
> timescales than what is observed for metal ions in aqueous solution.
> .......... Since typical MD simulation timescales are at the nanosecond or
> microsecond levels (circa 2014), the bonded model is an effective approach
> to study processes where ligand exchange does not occur over the timescales
> employed.'
>
> Though the Mn2+ ion in my protein do suggested to have CN switching during
> the catalysis, I am aiming for only about 100ns simulation to find out the
> role of some water molecules in the ligand-ion interaction. So I just
> wonder which model will be best fit in my case.
It depends on the question you are trying to investigate: which kind of role do you expect to see about some waters to the ligand-ion interactions? Does the water directly coordinated
to the ion?
Pengfei
>
> Any suggestions would be very much appreciated.
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Received on Fri Jan 29 2016 - 07:30:09 PST
