Re: AMBER: surface code in Amber

From: David A. Case <>
Date: Sun, 26 Oct 2003 22:45:18 -0800

On Sun, Oct 26, 2003, John Lee wrote:
> Thanks for the reply. I got the paper about LCPO and the code
> (gbsa.h) in AMBER. I found, in fact, it calculats all the atoms
> accessible area to get the solvent-accessible area by (do i=1,natom...).
> Here natom is the atom number in the whole protein. But what if there
> is a cave inside of the protein and the space is big enough to
> contains the probe ball. While there is no water can come into that
> cave actually. Thus the solvent-accessible area will be wrong. I am
> not sure about the interpretation. Am I right? or there are some other
> code that only calculate those atoms close to the surface in gbsa.h
> and I didn't catch it?

As with many surface area algorithms, the LCPO model does not distiguish
between "interior" and "exterior" solvent accessibility. (That is, you
have read the code correctly.)


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Mon Oct 27 2003 - 07:53:03 PST
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