Re: AMBER: Ti of CH3 -> NH2

From: David A. Case <>
Date: Wed, 7 Apr 2004 18:17:30 -0700

On Thu, Apr 08, 2004, Carsten Detering wrote:
> I have a question concerning the thermodynamic integration of a methyl group
> into a NH2 group: what happens to the hybridization of the heavy atom? The
> type changes from c3 (sp3 carbon with three hydrogens) to n2 (sp2 nitrogen
> with two hydrogens), the hydrogens from hc to hn. How should I handle the
> angles/dihedrals in both cases for the frcmod file? SHould I give
> tetrahedral angles for the c3 case, and trigonal-planar for n2? What about
> the dummy atom? What would be the torsion angle for it? Or is it only
> possible to change the CH3-group into a sp3-NH2 group?

"Hybridization" is a concept that is really peripheral to the force field.
You should set the parameters for the "0" and "1" states that match what
geometries you think they should have. The program won't care whether you
are changing sp3 to sp2 or not.

The question of getting good force field parameters for aniline-like NH2
groups is a separate issue, but a difficult one. The C-N bond is neither
single nor double, so that the geometry about the N atom is difficult to
describe. You just want to do the best you can, then make sure that the
parameters in the final state (NH2 + dummy atom) match your best estimate of
what that structure should be.

....good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Thu Apr 08 2004 - 02:53:00 PDT
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