Re: AMBER: double bonds in prmtop

From: David A. Case <>
Date: Fri, 19 Sep 2003 15:42:23 -0700

On Fri, Sep 19, 2003, Herbert Georg wrote:
> Ok, but my doubt is: if I have a chain like this
> C -- C == C -- C
> all of them are sp2 carbons but the bonds are different. I could have
> likewise
> C == C -- C == C
> Does amber attribute the same R0 and K_R to the bonds or it recognizes
> where are the double bonds. If it recognizes, how does it do it?

Remember that (with the exception listed below) amber doesn't "recognize"
anything. All of the templates in the libraries were made by humans who
coded in the parameters for the types of bonds that were there. As pointed
about elsewhere, there is no concept of a "bond order" inside amber.

The exception is the Antechamber program, which can "perceive" or recognize
chemical types based on an input structure. The way in which it handles
situations like the one mentioned above will be described in a paper that is
about to be submitted. The particular "polyene" vs "aromatic" collection
of sp2 carbons is indeed a tricky problem to handle in a fully general way.


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 Fri Sep 19 2003 - 23:53:00 PDT
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