Re: AMBER: antechamber and bond type

From: David A. Case <>
Date: Sat, 25 Oct 2003 19:49:05 -0700

On Wed, Oct 22, 2003, Herbert Georg wrote:

> I have used antechamber (amber7) with gaff to produce a prep file with
> bcc charges in a molecule that have a chain of alternate single and
> double bonds. As the manual says, the default operation is to assign
> both atom types and bond types, but in the simulation all of the C-C
> bonds are trated alike, as I can see from the bond lengths evolution in
> ptraj. Am I doing something wrong?

This problem will be fixed with some new atom types in version 2 of the
gaff force field.


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Mon Oct 27 2003 - 07:53:02 PST
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