I suppose you could start by binding a single monomer A to another monomer A'.
Then you could bind another monomer named A'' to the dimer (A,A') complex, and so on. And the likewise for the trimer, and so on.
The mechanism and free energy differences may be different for each of these steps, right? The tricky question is the size of the monomer unit A. If it's something relatively small, you can do all the above simulations. If it's larger -- say a capsid protein in a virus -- then it's harder to do those simulations, just because of simulation time.
Without knowing what your monomer is, it's hard to say. It also might be beyond the charter of the mailing list to design in detail the simulations you're talking about, but hopefully the above comments make sense.
Best of luck,
Nicholas Musolino
---------------------------------------------------------------------------
Nicholas Musolino
Ph.D. candidate, Department of Chemical Engineering, MIT
musolino.mit.edu | 617-253-6675 | Room E19-528
On Apr 20, 2010, at 7:45 AM, vijayaraj.clri.res.in wrote:
> Dear amber users,
>
> Is it possible to calculate the binding free energy for a oligomeric
> system, which is a self assembly of monomeric units.
> say, I have a monomer A, which forms a ordered structure by self assembling.
> In this case, there is no ligand - receptor complex. Its just a
> supramolecular assembly.
> I would like to see how the binding energy various when we increase the
> oligomerization.
>
> Thanks in advance.
>
> regards,
> vijay
>
>
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Received on Tue Apr 20 2010 - 05:00:06 PDT
