AMBER Archive (2003)

Subject: Re: AMBER: antechamber and bond type

From: David A. Case (case_at_scripps.edu)
Date: Sat Oct 25 2003 - 21:49:05 CDT

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.

..dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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