AMBER Archive (2009)

Subject: Re: [AMBER] ff parameters

From: case (case_at_biomaps.rutgers.edu)
Date: Thu Jul 09 2009 - 08:23:31 CDT

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

> Â 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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