AMBER Archive (2004)

Subject: AMBER: question about MGB and PB

Date: Fri Dec 10 2004 - 16:12:30 CST

Dear All,

I am really lost in comparing MGB and PB. I reand the original paper
about MGB(J. chem. phys. 1998-109-1465) and two David's papers(J
comput chem 2004-25-265 and 2004-25-238), still don't get it. My
question is:

when we compare MGB and PB,

1. should we set up internal dielectric =2 for solvation energy in
both methods? (my answer is "yes")

2. should we use internal dielectric =1 or 2 or (1 for MGB and 2 for
PB) for coulombic energy calculation? I think it also should be 2 for
both methods, but it was 1 in the original paper, and in,
the default GB method is MGB with default internal dielectric =1.
there is an internal dielectric option for PB, but not for GB, the
only way to change it for GB is to change the source code(thank
Fabien). So I think there must be a reason that Holger set up the
default GB method--MGB with the default internal dielectric=1.

Can anyone give me a hint about these questions? Thank you so much in



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