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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>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Tue Apr 05 2011 - 11:30:05 PDT
