Re: [AMBER] Stability calculations from MMGB/PBSA

From: David A Case <>
Date: Wed, 11 Nov 2015 07:59:37 -0500

On Wed, Nov 11, 2015, Rajeswari A. wrote:

> I did protein and its mutants simulations. I wanted to calculate the
> ralative stability of mutant protein with respect to wild type protein.

You should think carefully about the term "stability". It generally (but not
always) refers to something like the free energy of folding. If that is what
you are interested in, you would need to estimate (either via simulation or by
some model) the effect of mutation on the unfolded state as well as the folded

Generally, you will always need to construct a thermodynamic cycle, with two
wild-type entries and two mutant entries. The free energy change of just
making a mutation in one state (e.g. the folded state) is not well-defined.


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Received on Wed Nov 11 2015 - 05:00:08 PST
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