AMBER Archive (2003)

Subject: Re: AMBER: surface code in Amber

From: David A. Case (case_at_scripps.edu)
Date: Mon Oct 27 2003 - 00:45:18 CST

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 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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