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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Received on Sun Nov 25 2007 - 06:07:28 PST
