On Thu, Feb 27, 2014, Gargi Borgohai wrote:
>
> I am trying to generate an .frcmod file for a particular urea model. For
> that model *angle force constant* (i.e. k for angle O-C-N ) value is found
> to be 690 kj/mol in the literature. But to fit in AMBER format the unit
> should be in kcal/mol/degree square. What are the conversion rules to
> obtain the AMBER format?
Both things above sound incorrect. Amber uses kcal/mol-radian^2 for its angle
force constants, and I suspect your literature value is really also in
kJ/mol-radian^2. But you need to also check for a factor of 2: Amber
treats the angle energy at k*(theta-theta0)^2. "Literature" values might
do that, or might treat the energy as (1/2)k(theta-theta0)^2.
...dac
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Received on Thu Feb 27 2014 - 05:00:03 PST
