On Thu, Apr 26, 2012 at 2:06 PM, Jesper Sørensen <jesorensen.ucsd.edu>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
http://ambermd.org/vdwequation.pdf
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 "xparmed.py"
(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.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Apr 26 2012 - 12:30:03 PDT
