RE: AMBER: dihedral parameters

From: Jardas sucuriba <>
Date: Wed, 13 Jun 2007 02:18:12 +0000

Thanks D. Case. I am confused about the way the PK is calculated. I read the parameter development section in the amber8 manual and I understood the first two examples (CH3-CH3 and CH2-CH2) for dihedral parameters. However, in case of the ZH2C-CH2Z example I don┤t understand how the PK values are calculated. For instance, in figure3, the rotational barrier for v3~0.75 kcal/mol and so, I would expect that the PK = ~0.75/2=0.375. However PK for v3 is 0,260. How is this value exactly calculated?

> Date: Tue, 12 Jun 2007 12:35:57 -0700> From:> To:> Subject: Re: AMBER: dihedral parameters> > 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).> > ...dac> > -----------------------------------------------------------------------> The AMBER Mail Reflector> To post, send mail to> To unsubscribe, send "unsubscribe amber" to
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Received on Wed Jun 13 2007 - 06:07:38 PDT
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