Re: AMBER: dihedral parameters

From: David A. Case <>
Date: Tue, 12 Jun 2007 12:35:57 -0700

On Mon, Jun 11, 2007, Jardas sucuriba wrote:
> I used gaff to generate parameters for a ligand. However, for two dihedral
> angles, I want to use parameters already published. Those published
> parameters were calculated considering atom types derived from antechamber.
> It is provided the magnitude, phase and periodicity and now I want to add
> these parameters to the frcmod file. Is magnitude the same as the barrier
> height referred in the format for the dihedral parameters
> ( If so, do I
> have to divide the magnitude by 2?

Without knowing the details of the "already published" parameters, it is
impossible to say what those authors meant by the term "magnitude". So, only
you can tell the connection between "magnitude" and barrier height
(by reading the paper closely, I would imagine, or perhaps by
contacting the authors if that fails).


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Received on Wed Jun 13 2007 - 06:07:34 PDT
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