Re: [AMBER] Entropy calculation for a protein homodimerization

From: Pratul Agarwal <>
Date: Wed, 15 May 2019 11:47:16 +0000

In my group's experience, comparison with experimental data has shown that quasi-harmonic and normal mode calculations do not provide good estimations of the change in entropy. These calculations only provide very rough approximations, and depend on a number of factors. First, for many proteins the largest contributions to entropy change comes from protein motions that are anharmonic. Second, calculated values can significantly vary with the time-scale of MD. Third, calculated values can also depend on the starting structure(s) of MD.

Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)

On 5/15/2019 4:47 AM, Rakesh Srivastava wrote:

Hello all, I am studying the dimerization of two protein monomers which are
identical and each has 160 amino acids. In this study, I want to calculate
the entropy change taking place as a result of dimerization. In Amber,
there are two methods for entropy calculation, quasiharmonic and nmode
analysis. I want to know which method I should use and also please let me
know if there are tutorials available for entropy calculation.

Thanks in advance.

Rakesh Srivastava
Research Fellow
School of Computational & Integrative Sciences
Jawaharlal Nehru University, New Delhi-110067
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Received on Wed May 15 2019 - 05:00:06 PDT
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