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
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Apr 05 2011 - 11:30:03 PDT
