if you choose properly then it won't matter. i think the best method
is to use more atoms in the group-- too few atoms, and you might pull
them away from their local contacts, which won't really move the whole
domain. but it's really imposible to help any more since only you know
what motion you are trying to study. umbrella sampling is not a good
way to determine the motion- only to get an energy profile along a
motion path that you already have determined.
On Tue, Apr 5, 2011 at 2:21 PM, Sangita Kachhap <sangita.imtech.res.in> wrote:
> Thanks for reply
> Here I have to define reaction coordinate i. e. distance or angle (pathway)for
> whole protein or for a perticular key residue as given in Amber manual?
>
>
>> yes this is the sort of thing that you could address with umbrella sampling.
>> the key is not to define residues, but a pathway. You need to have an
>> idea of how to mathematically describe the process, and then umbrella
>> sampling can give the free energy along that process. the results are
>> only good if the pathway was defined well. if you pick a wrong path,
>> or wrong measure of the structure change, then the results may not be
>> meaningful.
>>
>> nobody can tell you the "best" measure of opening. it will take
>> insight into your system and how it works. One suggestion would be to
>> sonsider using a distance or angle restraint, probably with centers of
>> mass defined by groups of atoms, rather than distance between
>> individual atoms.
>>
>>
>> On Tue, Apr 5, 2011 at 1:55 PM, Sangita Kachhap <sangita.imtech.res.in> wrote:
>>>
>>> Hello all
>>>
>>> I have a protein-DNA complex which exist in active and inactive conformation.
>>> In
>>> active conformation it binds to DNA.
>>> Closed inactive conformation undergoes large conformational changes to get
>>> open
>>> active conformation.
>>> This protein have two domains reciever domain and DNA binding domain linked by
>>> linker helix.
>>>
>>> Its full length inactive and DNA bound active only DNA binding domain
>>> (structure) is availabel.
>>>
>>> I have done simple MD run and its very tough to get large conformational
>>> change
>>> by it.
>>>
>>> So I am thinking here to use Umbrella sampling.
>>>
>>> Is it possible here to use Umbrella sampling?
>>>
>>> Since as I have got through Amber manual there is requirement of defining
>>> reaction coordinate.Here I have to define reaction coordinate for a perticular
>>> residue or I can define for whole protein residues like in REMD?
>>>
>>> So anyone please suggest me.
>>>
>>> With regard
>>>
>>> Sangita Kachhap
>>> JRF
>>> BIC,IMTECH
>>> CHANDIGARH
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Apr 05 2011 - 11:30:05 PDT
