Re: [AMBER] ff parameters

From: case <case.biomaps.rutgers.edu>
Date: Thu, 9 Jul 2009 14:23:31 +0100

On Wed, Jul 08, 2009, oguz gurbulak wrote:

> I study on molecular dynamics simulations. I easily found all
> parameters for a pyrimidine and a benzene separately but I couldn't find
> some bond, angle and dihedral parameters between pyrimidine and benzene
> rings when they are connected to each other as in the figure. For
> example I couldn't find the dihedral parameter for CA-C!-C!-N . Could
> you please help me to learn these parameters ?

You can use antechamber and gaff to get some initial values; but these should
really be refined by doing a QM energy profile about the central bond, then
fitting your torsional parameter to that. This is a tough molecule to handle
in any automated fashion.

...good luck...dac


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Received on Thu Jul 09 2009 - 10:09:17 PDT
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