AMBER Archive (2008)

Subject: Re: AMBER: PB Radii

From: Swarup Gupta (swarupgupta_at_yahoo.com)
Date: Sat Nov 15 2008 - 21:44:25 CST

Thank a lot for your response.
 
Now I wish to know if I use igb=2 or igb=5 keeping the default dielectric radii set then the result would be worng or not reliable at all? I am trying to calculate binding free energy from MMGBSA calculation by postprocessing a trajectory which was originally run with explicit water.
 
regards,
S Gupta 
 

--- On Thu, 11/13/08, David A. Case <case_at_biomaps.rutgers.edu> wrote:

From: David A. Case <case_at_biomaps.rutgers.edu>
Subject: Re: AMBER: PB Radii
To: amber_at_scripps.edu
Date: Thursday, November 13, 2008, 6:01 AM

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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