A protein-protein complex (Ras-Raf) is actually used as one of the example
systems in the MMPBSA tutorial (
http://ambermd.org/tutorials/advanced/tutorial3/), so this is definitely a
legitimate way of treating the system. More details about the approach can
be found by looking at the reference for the MMPBSA on this system: Gohlke,
J Mol Bio., 2003, pgs. 891-913.
Good luck!
-Bill
On Sat, May 28, 2011 at 5:03 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi everybody,
>
> This is a general question regarding the applicability of MMPBSA for a
> particular problem which I summarise below.
>
> I'm dealing with a number of related crystallographic models whose
> biological unit is in dimeric form. The monomers are in the range of 125-140
> residues.
>
> The area of the dimer interface is small and not well conserved. This has
> led to the suggestion that dimerisation is an artifact of the
> crystallisation process. On the other hand biochemical experiments have
> established the existence of dimers under particular conditions.
>
> My question is the following. Is it legitimate to treat chainA as the
> receptor, chainB as the ligand, the dimer as the complex and subject them to
> MD followed by the use of MMPBSA.py to derive Gibbs free energies of
> binding? Are there any caveats in using such an approach.
>
> Many thanks
>
> George
>
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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Sat May 28 2011 - 05:00:03 PDT
