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
==================================================================
Received on Fri Dec 06 2002 - 13:11:13 PST
