Thanks, Dr. Pratul for providing the information.
Rakesh Srivastava
Research Fellow
School of Computational & Integrative Sciences
Jawaharlal Nehru University, New Delhi-110067
India
On Wed, May 15, 2019 at 5:17 PM Pratul Agarwal <pratul.agarwal-lab.org>
wrote:
> 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)
> Web: http://www.agarwal-lab.org/
>
>
> 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
> India
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Received on Wed May 15 2019 - 05:30:02 PDT
