AMBER Archive (2004)

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

From: David A. Case (
Date: Thu Dec 30 2004 - 21:55:59 CST

On Thu, Dec 30, 2004, Ilyas Yildirim wrote:
> Name Type Charge Element Pert.type Delta.charge
> O2 O -0.6252 O N2 N* (a number)
> DH1 0.0000 ? H12 H (a number)
> DH2 0.0000 ? H22 H (a number)

You have to give atoms DH1 and DH2 at type, probably a dummy ("DU")

> FATAL: Atom .R< 15>.A<DH1 1> does not have a type.
> FATAL: Atom .R< 15>.A<DH2 2> does not have a type.

This error is caused by the lack of type above.

> As far as I understood, we need to first create input files for leap using
> antechamber.

You can't use antechamber with dummy atoms. You can get parameters for the
beginning and end states, then enter them by hand into the perturbation

....good luck....dac

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