AMBER: frcmod file and NONB for dummy atoms

From: Ilyas Yildirim <>
Date: Thu, 22 Nov 2007 19:48:31 -0500 (EST)

Dear All,

The format of the frcmod file in

says that to define NONB terms for the new atom types, follow 10A, B or C.
For dummy atoms, we want this NONB term to be zero. In my frcmod file, I
have the following lines to define this NONB terms for the dummy atoms:

  DH 1.0000 0.000

I have tested this way of definition and it gives zero vdw energy for the
dummy atoms.

My question is the following: According to the format described in the
above website, someone has to define NONB in the following ways:

(Slater-Kirkwood parameters are input)


(van der Waals radius and the potential well depth)


(The 6-12 potential coefficients)

My question is, what is the right way to define this NONB terms? In DAC's
TI tutorial, he also defines these NONB parameters without using SK/RE/AC.
Thanks in advance.

Best regards,

  Ilyas Yildirim
  = Department of Chemistry      -                              =
  = University of Rochester      -                              =
  = Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) =
  =                     =
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Received on Sun Nov 25 2007 - 06:07:28 PST
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