AMBER Archive (2003)

Subject: Re: AMBER: surface code in Amber

From: David A. Case (case_at_scripps.edu)
Date: Tue Oct 28 2003 - 18:15:33 CST

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 

-- 

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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
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