On Sat, Jul 10, 2010, Xioling Chuang wrote:
> I used gaussian output to generate forcefield parameters using
> antechamber in AmberTools 1.3. My molecule is a DNA analogue. In frcmod
> file I got the same dihedral with different values of parameters, some
> part of frcmod file is listed below.
>
>
> CT-N*-CM-H4 1 0.625 180.000 2.000 same as X -c2-na-X
> CT-N*-CM-CM 1 0.625 180.000 2.000 same as X -c2-na-X
> CT-N*-C -NA 1 1.450 180.000 -2.000 same as X -c -na-X
> CT-N*-C -NA 1 0.350 180.000 4.000 same as X -c -na-X
> CT-N*-C -O 1 1.450 180.000 -2.000 same as X -c -na-X
> CT-N*-C -O 1 0.350 180.000 4.000 same as X -c -na-X
>
> Since this is one molecule, is it possible to get the same dihedral with
> different parameters (lines 3 & 4, as well as lines 5 & 6)?
Yes, this is normal. Many dihedrals have multiple parameters. In you
examples, one of the terms has n=2, the second has n=4. The sum of these
two Fourier terms is the full potential. You will see lots of such examples
in a "regular" parm.dat file, such as parm99.dat
....dac
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Received on Sat Jul 10 2010 - 07:00:03 PDT
