Hi Jason,
Thanks, I found those flags now.
%FLAG LENNARD_JONES_ACOEF
%FLAG LENNARD_JONES_BCOEF
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.
Thanks,
Jesper
On Apr 26, 2012, at 12:18 PM, Jason Swails wrote:
> 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 - 13:00:02 PDT
