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

From: Karen Callahan <>
Date: Mon, 6 Aug 2007 21:13:27 -0700 (PDT)


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

Also, in the case where specific bond lengths, angles,
connectivity and the Lennard-Jones parameters of the
atoms are described in a frcmod file what does naming
a hybridization in the Leap input actually do?

In the case where bonds are held rigid, or for a
monatomic ion, does the hybridization in the Leap
input file have any meaning?

Thanks in advance,
Karen Callahan

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Received on Wed Aug 08 2007 - 06:07:32 PDT
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