AMBER Archive (2005)

Subject: Re: AMBER: Dummy Atoms: How to create them?

From: David A. Case (case_at_scripps.edu)
Date: Tue Jan 11 2005 - 23:54:02 CST

On Wed, Jan 05, 2005, Ilyas Yildirim wrote:

> For atom: .R<C 14>.A<DH1 31> Could not find type: DU
> For atom: .R<C 14>.A<DH2 32> Could not find type: DU
> Parameter file was not saved.
> --------------------------------------------------------------------
> Does that mean that there is no dummy atom type defined in leaprc.ff99?

yes.

> If not, how should I define it? Creating an frcmod file?

yes.

  We are hoping to get a detailed tutorial out soon. Until then, you
will have to do some experimenting to see how dummy atoms work in free energy
calculations.

...dac

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