On Wed, Sep 11, 2013 at 5:29 AM, Mannan <malie_03.yahoo.co.in> wrote:
>
>
>
> Dear Amber users
>
> Will it be possible to do computational scanning for other residues other
> than just Alanine (ie, Leu, Ile, Trp, Phe), with the existing computational
> alanine scanning code in Amber
>
AmberTools 13 also supports glycine scanning. There are notable challenges
for residues with larger side-chains, because a decision must be made about
where to put that sidechain. Furthermore, if a new amino acid does not fit
where the original one did, the assumption that the conformations are the
same (which is implicitly assumed by mutating a residue in-place like the
MMPBSA.py alanine scanning code does) significantly weakens.
Alanine and glycine scanning is so easy because you just delete the 'extra'
atoms from the original side-chain until the alanine resides exactly where
the original residue was. Same thing with glycine. If you want to add
something big like a Trp or Tyr, you will likely have to re-run your
dynamics.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 11 2013 - 05:30:02 PDT
