AMBER Archive (2006)

Subject: Re: AMBER: How to set Bondi Radii using xleap. .

From: Don.Bashford_at_stjude.org
Date: Tue Aug 01 2006 - 12:23:51 CDT

>>>>> "Ilyas" == Ilyas Yildirim <yildirim_at_pas.rochester.edu> writes:

    Ilyas> Another question is the following: When the bondii radii
    Ilyas> for a specific type is set to zero, and igb=2 is used, I am
    Ilyas> getting NaN results in the output file (when bondii radii
    Ilyas> is not zero - even when it is very close to zero - the
    Ilyas> result is ok). I was wondering why this is creating a
    Ilyas> singularity in the system when implicit solvent is
    Ilyas> used. Thanks in advance.

The standard formulae of GB theory include terms like 1/a_i, where a_i
is the radius of atom i, so I think a NaN is to be expected. As long
as atom i has any possiblity of being exposed to solvent, a radius of
zero is unphysical because the energy of moving a point charge from
one dielectric medium to another diverges to infinity in the limit of
a zero-sized point.

-Don

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