Re: [AMBER] Radii in prmtop

From: case <>
Date: Thu, 26 Apr 2012 21:46:26 -0400

On Thu, Apr 26, 2012, Jesper Sørensen wrote:
> 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.

That is because delphi and APBS are electrostatic programs, looking for what
is most precisely called the intrinsic electrostatic radii, and just called
"RADII" in the prmtop file. I agree that a better name for that section could
have been chosen.


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Received on Thu Apr 26 2012 - 19:00:03 PDT
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