AMBER Archive (2007)

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

From: David A. Case (case_at_scripps.edu)
Date: Sat Aug 11 2007 - 15:35:15 CDT

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.

....dac
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