Re[2]: AMBER: surface code in Amber

From: John Lee <g03.joyie.com>
Date: Sun, 26 Oct 2003 18:06:56 -0800

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?

-- 
Best regards,
John Lee                            
Friday, October 10, 2003, 3:25:45 PM, you wrote:
AO> Hi, John.
AO> Yes, by setting gbsa=1, amber will compute (approximate)
AO> solvent-accessible area [A^2] using LCPO method.
AO> The resuly will be multiplied by SURFTEN (default 0.005 kcal/mol/A^2) and
AO> output as, I believe, SURF in the energy breakdown.
AO>                                         Hope that helps,
AO>                                                 Alexey
AO> On Sun, 5 Oct 2003, John Lee wrote:
>> Hi amber,
>>
>>   Is there any surface code in Amber that generate VDW surface or
>>   molecular or solvent-excluded surface? If not where I can find the
>>   code, better in Fortran.
>>
>> --
>> Best regards,
>>  John
>>
>>
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Received on Mon Oct 27 2003 - 07:53:03 PST