AMBER Archive (2003)

Subject: Re[2]: AMBER: surface code in Amber

From: John Lee (g03_at_joyie.com)
Date: Tue Oct 28 2003 - 00:53:49 CST

Hi David, Dave and AMBERS,

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? 

-- 
Best regards,
John Lee                            

Sunday, October 26, 2003, 10:45:18 PM, you wrote:

DAC> 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?

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

DAC> ..dac

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