AMBER Archive (2008)

Subject: Re: AMBER: igb and ibelly

From: David A. Case (case_at_scripps.edu)
Date: Fri May 30 2008 - 15:20:52 CDT

On Fri, May 30, 2008, Holly Freedman wrote:

> Can someone please explain to me why it is that the ibelly option is not
> allowed with igb>0 (Generalized Born)? I don't understand how the two
> options are connected.

Since GB is not a pairwise theory, it is not a simple matter to simply try to
ignore certain atoms. A discussion of what would be involved, and the
approximations required, is given here:

%A O. Guvench
%A J. Weiser
%A P. Shenkin
%A I. Kolossvary
%A W.C. Still
%T Application of the Frozen Atom Approximation to the GB/SA Continuum Model
for Solvation Free Energy
%J J. Comput. Chem.
%V 23
%P 214-221
%D 2002

These ideas have never been implemented in Amber.

You can set ntr=1 and restrain atoms to be (very) near to their starting
points.

[Aside: I've long been in favor of removing ibelly for any purpose in Amber,
but it hasn't been a high priority, and people seem to have some use for that
facility, so it still sticks around.]

...dac

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