Re: [AMBER] Stability calculations from MMGB/PBSA

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 11 Nov 2015 08:33:32 -0500

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 Wed Nov 11 2015 - 06:00:04 PST
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