Hi Anu,
Sorry for the late reply. For your situation I recommend you to use nonbonded model.
This is due to that bond breaking could not happen when using the bonded model: the bonded model can only help you to see the bond vibration in the metal site.
And if you want to study chemical reaction happened during the simulation, it is better to use the QM/MM approach since generally pure MM method is not suitable to study chemical reactions.
Hope it helps,
Pengfei
> On Jan 29, 2016, at 5:56 PM, anu chandra <anu80125.gmail.com> wrote:
>
> Hi Pengfei,
>
> Many thanks for your reply.
>
> On Fri, Jan 29, 2016 at 3:15 PM, Pengfei Li <ambermailpengfei.gmail.com <mailto:ambermailpengfei.gmail.com>>
> wrote:
>
>> Hi Anu,
>>
>>
>>> On Jan 29, 2016, at 9:26 AM, anu chandra <anu80125.gmail.com <mailto: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.
>>
>
> Yes. The Mn2+ ion helps its coordinated residue to nucleophilically attack
> the substrate, which eventually leads to the release of product.
>
>
>>
>>> 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?
>
>
> Sorry for not being specific here. My immediate objective is to explore the
> role of some conserved water molecule in the ligand binding pocket,
> especially in positioning the ligand. The water is not coordinated with the
> ion. The ion in this case is coordinated with the substrate and
> neighbouring amino acid residue.
>
>
>> Pengfei
>>
>
> Many thanks
>
> Anu
>
>>
>>>
>>> Any suggestions would be very much appreciated.
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>>
>>
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Received on Wed Feb 03 2016 - 08:30:03 PST
