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.)
...dac
--
==================================================================
David A. Case | e-mail: case.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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Received on Mon Oct 27 2003 - 07:53:03 PST
