AMBER Archive (2002)

Subject: Re: default GB radii

From: David A. Case (case_at_scripps.edu)
Date: Fri Dec 06 2002 - 15:11:13 CST

On Fri, Dec 06, 2002, Robert G. Endres wrote:
>
>
> does anyone know where I can find the default GB radii, or are these the
> vdW radii in e.g. parm99.dat?

Values depend on which GB model you are using. See pp. 60-61 (and also p. 90)
in the Users' Manual. Recommended values are *not* the vdW radii, but are
mostly modifications of Bondi radii.

Also note the following correction to the manual (from the amber web site):

p. 60
The references to gblambda under PBradii are incorrect. We recommend using
bondi when igb=2, and mbondi when igb=1. 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================