AMBER Archive (2006)

Subject: AMBER: Born igb =2

From: harianto (harianto_at_mailer.sb.fsu.edu)
Date: Mon Apr 24 2006 - 20:27:24 CDT

Dear developers,
I've got a question regarding GB implemented by option igb=2 or igb = 5
(amber8), are they parameterized based on the molecular surface or vdW
surface? I know the integration (for obtaining psi) is over vdW volume,
but I'm not sure about the alpha, beta and gamma are parameterized. The
significant of my question is when I want to make comparison GB (igb
=2,5) to PB calculation, whether or not I should use molecular surface
for PB.
Thank you.
Regards,
Harianto.

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