Re: AMBER: How to set Bondi Radii using xleap

From: David A. Case <>
Date: Tue, 1 Aug 2006 10:17:38 -0700

On Tue, Aug 01, 2006, Ilyas Yildirim wrote:
> Is there any way to set the bondii radii to zero or any value for a
> specific atom type using xleap?


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

You can't use a zero radius for any atom with a non-zero partial charge: that
would create real problems with the electrostatic energies. Even for atoms
with zero partial charge, using a zero dielectric radius is probably dangerous
(as you have found), since the code was certainly never carefully checked for
this possibility.


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Received on Wed Aug 02 2006 - 06:07:13 PDT
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