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

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 18 Jan 2011 13:26:52 -0500

This was a little script I wrote for myself to make this easier, so it's not
a robust, user-friendly application. I think it should be fairly
self-explanatory but if you have any questions, feel free to ask.

Good luck,
Jason

On Tue, Jan 18, 2011 at 1:20 PM, Millen, Andrea <andrea.millen.uleth.ca>wrote:

> Thanks very much Jason. If you could send me the script I would
> appreciate it!
>
> Andrea
>
> -----Original Message-----
> From: Jason Swails [mailto:jason.swails.gmail.com]
> 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
> 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
> >
> > _______________________________________________
> > AMBER mailing list
> > 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
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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> 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 Tue Jan 18 2011 - 11:00:04 PST
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