AMBER Archive (2005)

Subject: AMBER: Question about GAFF atom types

From: Herbert Georg (hcgeorg_at_if.usp.br)
Date: Thu Jun 16 2005 - 14:18:50 CDT

Hi, I'm trying to find the best choice of parameters to apply to a
sistem like

     CH3
          \
            N == quinone
          /
     CH3

I'm specially worried about the N, which is an amine N and makes 2 bonds
with a quinone ring. I'm worried also about the quinone carbon with
which the nitrogen bonds. I looked at the J. Comp. Chem. article and
also inside the parameter's file, gaff.dat, but couldn't decide for the
pair of atom types. For example If I set the N atom as "nh" and the C
atom as "c", I noticed that there are no parameters for the bond c-nh.
Any light on this would be wellcome.
Thanks,
Herbert
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