Hi Anu,
If you want to perform QM/MM study of the system, you can build a bonded model first, and you can use the structure after MM MD equilibration to begin the QM/MM study.
Pengfei
> On Feb 3, 2016, at 11:17 AM, Pengfei Li <ambermailpengfei.gmail.com> wrote:
>
> 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 <mailto: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 - 09:00:04 PST
