AMBER Archive (2006)

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

From: David A. Case (case_at_scripps.edu)
Date: Tue Aug 01 2006 - 12:17:38 CDT

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?

No.

> 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.

...dac

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