AMBER Archive (2009)

Subject: Re: [AMBER] Gly -> Ala mutation

From: manoj singh (
Date: Sun Nov 08 2009 - 13:14:23 CST

Thanks for your reply.

I understand the Gly can attain all PHI and PSI values, however other amino
acids can not. But, if the Gly is in "usual" conformation, is it possible to
mutate it to Ala using any available technique/script in the process of
performing MM-PBSA.

One more thing, when talking about electrostatic energy, one should not
forget desolvation energy.


On Sun, Nov 8, 2009 at 12:53 PM, Jason Swails <>wrote:

> Hello,
> You can write your own script/program to do the transformation. Soon there
> will be a release of a new MM-PB(GB)SA script for amber that should be
> faster and more user-friendly (and should handle alanine-scanning more
> easily). However, even this new script does not handle Gly-Ala mutations
> since this is more complex than every other mutation. For every other
> residue, all that is needed to handle an alanine mutation is to remove
> extraneous atoms and readjust some bond lengths to match those in alanine.
> Glycine is the only amino acid that has fewer atoms than alanine, so in
> order to perform that mutation, atoms would need to be added to the system.
> This is non-trivial, because the question becomes "where do we add those
> extra atoms?" (Ala has more degrees of freedom than Gly)
> It may even be the case that in a specific conformation, an alanine would
> not even fit where there's a glycine, so you would get an unphysically high
> penalty for mutating that residue. Thus, the short version, there is no
> clear-cut, systematic way to handle a Gly->Ala mutation, so it's not done.
> Furthermore, alanine scanning is designed more to measure the electrostatic
> (and perhaps VDW) effects that a particular sidechain has on the activity
> of
> a protein. Glycine (and proline, though Pro->Ala is an allowed mutation in
> the upcoming version if not this one) more often serves a role in
> modulating
> the structure of a protein, so alanine scanning is often ill-suited to
> probing the importance of a Glycine in the first place.
> Hope this helps,
> Jason
> On Sun, Nov 8, 2009 at 12:25 PM, manoj singh <> wrote:
> > Hi all!
> >
> > The can't do Gly->Ala mutation. Is there any way to do this
> > mutation in trajectory.
> >
> > Sincerely,
> > _______________________________________________
> > AMBER mailing list
> >
> >
> >
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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