On Jan 25, 2014 2:34 AM, "Jason Swails" <jason.swails.gmail.com> wrote:
>
> 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
>
>
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Received on Sat Mar 15 2014 - 21:00:02 PDT
