[AMBER] Question of Parameter Defaults

From: Robert Molt <rwmolt07.gmail.com>
Date: Fri, 12 Aug 2016 21:00:57 -0400

Good evening,

I am confused on an aspect of parameter values in the GAFF/Amber force
fields. Using defaults of ff14SB for a molecule I put through
Antechamber, the frcmod file has the value

CA-CA-CT-OS 1 0.000 0.000 2.000 same as X

for the above dihedral. My understanding is that the order of parameters
goes dividing factor, k force constant, n periodicity, phi phase angle.

I find it difficult to understand that any torsional potential is zero.
I could understand it being small, but zero seems un-physical. Do I
misunderstand which parameters correspond to what in

E=k cos (( n phi + psi) +1)

, or is my understanding of dihedral potential energy surfaces flawed
that zero values are realistic? Or is this just an example of a dihedral
parameter being zero because the total potential energy of the entire
force field parameterized in such a way that the component is not

Dr. Robert Molt Jr.
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Received on Fri Aug 12 2016 - 18:30:02 PDT
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