Re: [AMBER] Radii in prmtop

From: Jason Swails <>
Date: Thu, 26 Apr 2012 15:18:33 -0400

On Thu, Apr 26, 2012 at 2:06 PM, Jesper Sørensen <>wrote:

> Hi Carlos,
> Thanks for the clarification.
> Where are the radii specified then? I don't see them any place else in the
> prmtop, but maybe I am not looking in the right place.

They are combined in LEaP and printed out as A coefficients and B
coefficients. See

You would have to back out the Lennard Jones parameters by reversing the
combining rules on the A- and B-coefficient arrays to get the original well
depth and radius.

ParmEd (part of AmberTools 12) does this for you. You can use ""
(the GUI version) to load a topology file, then "printDetails" will take a
mask as input, printing all of the details for each atom selected by the
mask, including the LJ Radius, LJ Depth.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Thu Apr 26 2012 - 12:30:03 PDT
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