AMBER Archive (2008)

Subject: Re: AMBER: PB Radii

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu Nov 13 2008 - 06:01:57 CST

On Wed, Nov 12, 2008, Swarup Gupta wrote:

> I want to know if I use IGB=2 while keeping the default radii set then
> whether the results would be wrong!! The manual says that "With this option,
> you should use the LEaP command "set default PBradii mbondi2"......but my
> confusion is that I am not working with PB; then what is the use of setting
> a PBradii here while running GB?

The term "PBradii" might better be named "continuum_electrostatics_radii" or
"dielectric radii". They are used for both GB and PB calculations.

...dac

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