Re: [AMBER] Chirality of amines in GAFF

From: Jason Swails <>
Date: Wed, 14 Apr 2010 08:44:39 -0400


I believe this type of thing would be accounted for by an improper
dihedral term. If there is no improper dihedral term for this group,
you may have to create one via an frcmod to your molecule. I do not
believe this is done by default, though it's easy to check in gaff.dat
or your existing frcmod if you created one.

The path I'd tentatively suggest is to get the energy profile of
chiral inversion by using restraints and minimization via sander on
some type of model system with that group and then fitting an improper
term to adjust that profile to your target (maybe generated by a
quantum calculation...)

Of course others may chime in with better ideas, this is just the one
that popped to mind.

Good luck!

On Wed, Apr 14, 2010 at 3:43 AM, Dmitry Nilov <> wrote:
> Dear Amber community!
> Amines of the type NHRR' are chiral because of the lone pair of electrons.
> The energy barrier for inversion of stereocenter is about 7 klcal/mol.
> I wonder if there is some mechanism in GAFF to prevent the amine
> inversion. I suppose that 7 klcal/mol barrier crossing is a low-probability
> event on the time scale of MD simulations, nevertheless I've observed
> inversion of my amine during equilibration stage.
> Thanks in advance!
> --
> Dmitry Nilov,
> Lomonosov Moscow State University
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Wed Apr 14 2010 - 06:00:09 PDT
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