AMBER Archive (2005)

Subject: AMBER: atom type designation

From: Lihua Wang (lhw_at_broyde.nyu.edu)
Date: Fri Mar 04 2005 - 18:05:10 CST

Hi amber users,

I have a modified residue for which I need to provide force field
parameters. it is a 2-aminofluorene connected to C8 of a guanine. the
linkage site looks like:

     N7 H C==C
       \ | // \\
  Gua C8-N-C C--
       / \\ //
     N9 C==C AF
                  \

The double bonds refers to aromatic ring. Only part of the guanine and
part of the aminofluorene are given above.

I would like to know what atom type is the most appropriate for the
Nitrogen atom that links guanine C8 and the AF ring...(that is, the
middle N atom in above structure).

Possible candidates are N2 or N* in parm99.dat (after all what is the
difference between N2 and N* in this file?)

any comments or suggestions are welcome. thanks.

Lihua

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