Re: [AMBER] Stability calculations from MMGB/PBSA

From: Rajeswari A. <rajeswari.biotech.gmail.com>
Date: Thu, 12 Nov 2015 13:25:25 +0530

Thank you very much Carlos, David Case and Jason for your explanations and
suggestions.

Thanks once again.
On Nov 11, 2015 7:03 PM, "Jason Swails" <jason.swails.gmail.com> wrote:

> On Wed, Nov 11, 2015 at 3:54 AM, Rajeswari A. <rajeswari.biotech.gmail.com
> >
> wrote:
>
> > Dear all,
> > I did protein and its mutants simulations. I wanted to calculate the
> > ralative stability of mutant protein with respect to wild type protein.
> >
> > For that can i use MMGB/PBSA analysis specifying the protein as complex
> > (although it is a single entity)?
> >
> > Using MMGBSA, the resultant difference between mutant and wildtype is
> ~300
> > Kcal/mol. Is the difference acceptable? Please suggest.
> >
>
> ‚ÄčAs Carlos and Dave pointed out, you usually want to do a delta-delta G (as
> defined through some kind of thermodynamic cycle). The zero-point energy
> for a force field is undefined (in fact, it's probably different for each
> system), which means the only values that have any real, physical meaning
> are energy differences *of the same system*.
>
> Subtracting the energy of a wild-type protein conformation from the energy
> of a mutant protein conformation is a meaningless value. You can't compare
> single-point energies, or conformational average energies between different
> systems -- you can really only compare energy *differences* between
> different systems (i.e., a delta-delta G).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu Nov 12 2015 - 00:00:03 PST
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