AMBER Archive (2003)

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

From: John Lee (g03_at_joyie.com)
Date: Sun Oct 26 2003 - 20:06:56 CST


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 >> >> >> ----------------------------------------------------------------------- >> The AMBER Mail Reflector >> To post, send mail to amber_at_scripps.edu >> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu >>

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