On Thu, Oct 29, 2015 at 11:27 AM, Fabian gmail <fabian.glaser.gmail.com>
wrote:
> Hi,
>
> I am interested in calculating DDG for WT - MUTANT of a certain multi
> peptide system (32 identical peptides). But I cannot use the
> &alanine_scanning procedure in MMPBSA.py since I need to mutate not one but
> all 32 residues (one in each peptide) including on the ligand and receptor
> (31 and 1 peptide respectively). That cannot be done with MMPBSA.py I
> understand, which allows a single mutation.
>
> So I thought to repeat the whole MD and MMPBSA.py energy calculations,
> using a 32 ALA mutant receptor, complex and ligand, and then compare the DG
> of mutant and WT system (using exactly the same conditions).
>
> Is that a reasonable approach?
>
Yes.
> I mean will I get reasonable DDG (wt - mutants) prediction difference?
>
It should be better than alanine scanning in MMPBSA.py since it will add
the actual protein response to the mutations.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Oct 29 2015 - 09:00:04 PDT
