Re: [AMBER] Torsional parameters for S-C-C-N bond

From: Millen, Andrea <>
Date: Tue, 18 Jan 2011 11:20:12 -0700

Thanks very much Jason. If you could send me the script I would
appreciate it!


-----Original Message-----
From: Jason Swails []
Sent: Monday, January 17, 2011 10:00 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Torsional parameters for S-C-C-N bond

If you can find parameters someone has generated specifically for that
of torsion for a related system that was specifically generated for the
amber force field (with which gaff is compatible), then you can
test that value out and see if the distribution of sampled dihedral
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
very least, it'll show you how I set up amber input files so you can do
yourself. If you use this method, however, don't forget to set the
torsion potential to 0 via an frcmod or something.

Good luck!

On Mon, Jan 17, 2011 at 6:45 PM, Millen, Andrea

> 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
> MM and QM energies.
> What method is recommended? Thank you for any insights,
> Andrea Millen
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
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Received on Tue Jan 18 2011 - 10:30:04 PST
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