Re: AMBER: Radii for water hydrogens are different

From: David A. Case <>
Date: Fri, 19 Jan 2007 10:13:41 -0800

On Tue, Jan 16, 2007, Steve Spronk wrote:

> I stumbled upon what I think is an interesting bug in Amber 8. I used tLEaP
> to set up a system consisting of a protein solvated in TIP3P water, using
> ff03. The PDB that I used still had its crystallographic waters, and I used
> the solvateoct command to add a waterbox.
> In the prmtop file that tLEaP wrote out, the %FLAG RADII section showed that
> for the crystallographic waters, the radii for the hydrogens were 0.8 and
> 1.2. They had different radii.

Thanks for the report. We will try to see how to fix this. Note, however,
that these radii are not used for explicit solvent simulations, so that in
your case, the problem is innocuous.

Even for GB simulations (where the RADII are important), we have never
parameterized values for water itself. Still, the program should not be
putting out such weird values.


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Received on Sun Jan 21 2007 - 06:07:40 PST
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