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
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Received on Tue Apr 05 2011 - 11:00:05 PDT
