Re: AMBER: &dipoles output in QM/MM simulations

From: Adrian Roitberg <>
Date: Fri, 02 Nov 2007 09:06:28 -0400

Dear Seongeun,
I do not believe amber has at this point more advanced population
analysis, but they should not be too difficult to code. The full Fick
matrix is there, overlap, etc.

 From the Mulliken charges, a simple linear transformation would give
you CM3 charges (See papers by Cramer and Thrular on this). These have
been fond by people to better reproduce solvation energies, etc.

Now, I believe you want the charges to compute IR spectra, correlation
functions, etc. In that case, Mulliken might not be totally bad, in that
the frequencies can potentially come out all right, but your intensities
are probably suspect.

Just my 2 cents worth.


Seongeun Yang wrote:
>> From your email it seems that you would
>> be happy with QM dipoles calculated using mulliken charges so please try
>> applying the attached patch to your amber9 tree.
> Hi Ross, I missed something to add in my previous post.
> The reason I use mulliken charges is not because I'm happy with that.
> Is there any other pupulation analysis methods supported in amber qm/mm?
> I don't remember I saw other than mulliken's in the manual.
> Please let me know if there is some way to do advanced population analysis in amber, if any.
> But on the one hand I'm quite dubious about how much an advanced population analysis results
> would improve quantitatively in the semiempirical quantum mechanical level.
> Thanks.
> Seongeun
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                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry
University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email
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Received on Sun Nov 04 2007 - 06:07:41 PST
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