Re: [AMBER] Per-residue decomposition energy

From: Jason Swails <>
Date: Tue, 17 Mar 2015 08:45:47 -0400

On Tue, 2015-03-17 at 11:52 +0800, maryam azimzadehirani wrote:
> That was really helpful. Thanks. I was unaware of R (effective radii) as a
> sum for all atoms. I need to read more on this.

Qualitatively, it makes sense. Generalized Born is a generalization of
the Born solution to the Poisson equation
( It defines an "effective"
radius, which is basically the average distance from the charged atom
(a.k.a. the *ion*) to the surface of the dielectric boundary (with the
solute being a region with a low dielectric constant and solvent being a
region with a high dielectric constant).

In this case, the effective radius will obviously depend on its
immediate surroundings, since those surrounding atoms will exclude the
solvent from a larger region around that central atom. So removing a
residue between two atoms will affect the interaction between those two
atoms through its effect on their effective radii.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Mar 17 2015 - 06:00:02 PDT
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