Re: AMBER: Nmode vs QM Freq Calculation

From: David A. Case <>
Date: Wed, 1 Mar 2006 10:54:12 -0800

On Wed, Mar 01, 2006, Mark Williamson wrote:
> When one is parameterizing for a small molecule say using the GAFF, how
> useful is the comparison between frequencies obtained from NMODE for
> that parameterization, and the QM "normal mode" frequencies from say a
> HF/6-31G* Guassian "opt freq" calculation?

This is pretty useful if you want to see the limitations of the simple gaff
model, or as a starting point for improvements for individual molecules.
You might consider first applying a scaling factor to the Gaussian frequencies
(to bring them more into line with experiment), and/or using a DFT model like
B3LYP, which will generally have better frequencies.

...good luck...dac

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 Sun Mar 05 2006 - 06:10:12 PST
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