Re: [AMBER] sander option "-radii"

From: Jason Swails <>
Date: Tue, 30 Jul 2013 23:26:52 -0400

On Tue, Jul 30, 2013 at 9:14 AM, Soonmin Jang <> wrote:

> Dear amber users,
> In amber11 user manual, I see sander option "-radii" (page 21) but I am not
> able to find any explanation on it. Just curious.

My guess is that it is a historical flag, perhaps at one point allowing
people to input implicit solvent radii for GB/PB simulations. Since Amber
7 (ca. 2002, I think), the topology file itself has contained the implicit
solvent radii (look for RADII in any prmtop), so this flag was likely

It does not appear to be used anywhere. Not a single test in the test
suite uses it, nor does the file appear to ever be opened.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Jul 30 2013 - 20:30:03 PDT
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