AMBER Archive (2007)

Subject: AMBER: frcmod file and NONB for dummy atoms

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Nov 22 2007 - 18:48:31 CST

Dear All,

The format of the frcmod file in

http://amber.scripps.edu/formats.html#frcmod

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:

-------------------------------
NONB
  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:

NONB SK
(Slater-Kirkwood parameters are input)

or

NONB RE
(van der Waals radius and the potential well depth)

or

NONB AC
(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) =
  = http://www.pas.rochester.edu/~yildirim/                     =
  ---------------------------------------------------------------

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