Re: AMBER: hybridization in Amber, pertaining to resonant structures, ions

From: David A. Case <>
Date: Sat, 11 Aug 2007 13:35:15 -0700

On Mon, Aug 06, 2007, Karen Callahan wrote:
> In the Leap input file we specify hybridizations for
> atom types such as sp2 or sp3. I would like to know,
> in the case of a resonant structure, such as ozone or
> sulfate, how the atom-type's hybridization is
> determined.

Amber "Hybridization" is fixed for a given atom type, and is not dependent
on what sort of molecule the atom is embedded in.

> Additionally, how is hybridization
> determined for spherical ions which are not involved
> in covalent bonds?

Hybridization is irrelvant if there are no covalent bonds. I don't think it
matters what value is used.
> what does naming a hybridization in the Leap input actually do?

Very little. It triggers some warnings, and that is about it.

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Received on Sun Aug 12 2007 - 06:08:10 PDT
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