AMBER Archive (2003)

Subject: Re: AMBER: surface code in Amber

From: David E. Konerding (dekonerding_at_lbl.gov)
Date: Mon Oct 27 2003 - 09:32:41 CST

John Lee wrote:

>Hi Alexey and AMBERs ,
>
>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?
>
>
>
Are you sure the water can't access a "cave" in side a protein?

Normally, caves collapse due to VDW forces; if they don't, they're
something supporting them.
Furthermore, water (and even much larger ligands) can diffuse into proteins.

Dave

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