Re: AMBER: surface code in Amber

From: David A. Case <>
Date: Tue, 28 Oct 2003 16:15:33 -0800

On Mon, Oct 27, 2003, John Lee wrote:
> I just worried about if there is such a cave. And most possiblly caves
> collapse due to VDW forces. I think if there is a cave, it also can be
> overcome by increase the radius of the probe ball, I still didn't find
> the probe ball, may be it didn't exist.
> If there is no probe ball and the cave in the middle of
> the protein is not bigger than a probe ball. LCPO will still
> count on the surface area of the cave. Once we use the surface to
> assign the dielectric constant (inside surface is 4, outside is 80),
> don't you think that will cause some problem?

Note that the GB model has no concept of a probe sphere or of its radius.
The dielectric model and the solvent-accessible surface model are distinct
entities. So, the solvent accessible surface has nothing to do with
assignment of dielectrics.

Furthermore, in GB, "inside" has dielectric 1, not 4.

...hope this helps...dac

David A. Case                     |  e-mail:
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            |
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Oct 29 2003 - 00:53:01 PST
Custom Search