AMBER Archive (2006)

Subject: Re: AMBER: Nmode vs QM Freq Calculation

From: David A. Case (
Date: Wed Mar 01 2006 - 12:54:12 CST

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 | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to