Re: [AMBER] Stability calculations from MMGB/PBSA

From: Carlos Simmerling <>
Date: Wed, 11 Nov 2015 07:35:56 -0500

300 kcal/mol coudl be reasonable for the change in stability if the
mutation introduces a very unfavorable interaction that prevents the
protein from folding. Keep in mind that 300 kcal is a huge number.

it is possible to use MMGBSA, but it will of course be approximate. keep in
mind that for a stability calculation you probably want delta delta G,
which means you are doing calculations for 4 states (folded and unfolded
for wild type, folded and unfolded for mutant). how you set that up and
which terms you include in the delta G calculation will influence the
accuracy of your results. You also need to decide how to do the calculation
for the unfolded state - almost certainly you cannot sample over the entire
unfolded ensemble and need to make some approximations instead, such as
using a short peptide as a model for unfolded protein. You may also need to
make assumptions about the native structure of the mutants, unless you know
that from experiment.

On Wed, Nov 11, 2015 at 3:54 AM, Rajeswari A. <>

> 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.
> Thanks in advance
> --
> Rajeswari A,
> PhD Research Scholar,
> Computational Biophysics Lab,
> Department of Biotechnology,
> Indian Institute of Technology Madras,
> Chennai 600 036, Tamil Nadu, India.
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Received on Wed Nov 11 2015 - 05:00:04 PST
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