AMBER Archive (2004)

Subject: AMBER: Ti of CH3 -> NH2

From: Carsten Detering (
Date: Wed Apr 07 2004 - 17:14:11 CDT

Hi Ambers,

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?

Any helpful suggestions are appreciated


Carsten Detering
University of Washington
Department of Chemistry
Seattle, WA 98195
Fon 206.543.5081
Fax 206.685.8665

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to