AMBER Archive (2002)

Subject: Re: Dielectric constant for interior of proteins

From: Pratul Agarwal (pratulka_at_rocketmail.com)
Date: Thu Oct 10 2002 - 14:25:51 CDT

--- "David A. Case" <case_at_scripps.edu> wrote:
> There is no "quick" answer-- it depends entirely on what you are planning
> to do with the results, and how much explicit averaging of protein
> conformations you are including. Remember that a dielectric constant
> is a model for electrostatic relaxation. If you include this explicitly,
> you don't need a dielectric model.

I am writing an analysis program similar to anal, which will
calculate interaction energies between different residue pairs.
In short, I wanted suggestions for IDIEL/DIELC used with anal.
(The structures are obtained from 500 ps MD simulation with
explicit solvent.)

> The literature on this subject is quite extensive, and you might as well go
> ahead and read some of it.

I am. I thank you for your kind kind response.

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