AMBER Archive (2006)

Subject: Re: AMBER: Born igb =2

From: John Mongan (jmongan_at_mccammon.ucsd.edu)
Date: Tue Apr 25 2006 - 12:30:22 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.

These parameters were set to try to match the effective radii as closely
as possible to PB molecular surface effective radii (this is described
in the publication referenced in the manual). There is a limit to how
much of an improvement can be realized by a geometry-independent
rescaling, though, so igb=2 or 5 retains many of the properties of a vdW
surface, particularly for atoms near solvent.

The igb=7 model released with amber 9 gets somewhat closer to molecular
surface results by using a geometrically-based pairwise correction term,
but it is still a long way from perfect.

> 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.

I guess that depends somewhat on the purpose of the comparison, but my
general feeling is that the vdW surface definition is a sufficiently bad
approximation of reality that there are very few instances where you
would want to use it.

John
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