Re: [AMBER] Radii in prmtop

From: Jason Swails <>
Date: Thu, 26 Apr 2012 16:24:16 -0400

On Thu, Apr 26, 2012 at 3:56 PM, Jesper Sørensen <>wrote:

> Hi Jason,
> Thanks, I found those flags now.
> The reason I ask is that when you use ambpdb to write out a PQR file - to
> use with delphi or APBS, that prints out data from (%FLAG RADII), which is
> what confused me in the first place - as the radii were not what I expected
> them to be.
> ParmEd sounds like a nifty tool. I'll take a look at it.

It's described in the manual, but I wrote a little tutorial page on how to
use it and (some of) what it can do here:

(I had to advertise it somewhere :))

All the best,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Thu Apr 26 2012 - 13:30:02 PDT
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