On Fri, 2014-01-24 at 14:24 -0500, bharat lakhani wrote:
> Hi all
>
> Is it possible to do the binding free energy calculation if you mutate WT
> residue to all possible mutation other than ALA. I know we can do ala
> scanning.
MMPBSA.py also supports Glycine scanning. As Carlos says, it is trivial
to perform those mutations due to their lack of side-chain rotamers
(they are the two smallest amino acids).
Anything else you will actually have to perform the mutation and re-run
the simulations. Since proteins pack fairly densely, it is unlikely
that in-place mutations (like what is done with alanine and glycine)
will yield even qualitatively useful results, so no effort has been put
into enabling such mutations.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 24 2014 - 13:30:03 PST
