If you can find parameters someone has generated specifically for that type
of torsion for a related system that was specifically generated for the
amber force field (with which gaff is compatible), then you can certainly
test that value out and see if the distribution of sampled dihedral angles
are what you'd expect.
The second method is easy enough as well, and one that I've done a couple of
times myself. If you want, I can share a simple shell script that will
generate the torsion potential within amber (since you need to fit the
fourier terms to the QM - MM difference in the torsion potential). At the
very least, it'll show you how I set up amber input files so you can do it
yourself. If you use this method, however, don't forget to set the unknown
torsion potential to 0 via an frcmod or something.
Good luck!
Jason
On Mon, Jan 17, 2011 at 6:45 PM, Millen, Andrea <andrea.millen.uleth.ca>wrote:
> Greetings,
>
>
>
> I have a question about force field parameterization. I have a system
> that contains a "S-C-C-N" torsion angle which I need GAFF torsional
> parameters for. I have seen a couple of methods for doing this in the
> literature, such as scaling existing (GAFF) parameters from similar
> systems to approximate the QM energy profile for rotation about the
> angle, or methods based on minimizing the squared difference between the
> MM and QM energies.
>
>
>
> What method is recommended? Thank you for any insights,
>
>
>
> Andrea Millen
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Jan 17 2011 - 21:30:04 PST
