Re: [AMBER] Question of Parameter Defaults

From: Carlos Simmerling <>
Date: Sat, 13 Aug 2016 10:37:00 -0400

It's very possible for some terms in the Fourier series to be set to zero
amplitude. Whether it was zero or a small number may depend on how the
fitting was done, and the number of data points vs number of variables. If
you have a question about a specific term and how the fitting was done, you
could reply and the person that did the fitting may reply.

Setting amplitude for a specific periodicity to zero is also safer than
leaving it out - this way you're sure it didn't get set to another value
somewhere else, or left uninitialized.

On Aug 12, 2016 9:01 PM, "Robert Molt" <> wrote:

> 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
> -c2-c3-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
> meaningful?
> --
> Dr. Robert Molt Jr.
> _______________________________________________
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Received on Sat Aug 13 2016 - 08:00:02 PDT
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