Re: AMBER: AMBER citation questions

From: Carlos Simmerling <>
Date: Thu, 04 Jan 2007 06:36:28 -0500

The J. Comput. Chem. reference is correct for ff99.
Just for the record, though, I want to point out again that
ff99 for proteins has well-known and serious problems and people
should almost certainly not be using it. You are quite likely to
have reviewers of your article question your work if you
use ff99 for proteins. We have discussed these problems in the
following article, and others have also reported problems with ff99:


Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A. and
Simmerling, C., /“Comparison of multiple Amber force fields and
development of improved protein backbone parameters”/, Proteins:
Structure, Function and Genetics, 3:712-725 (2006). wrote:

>hello amber developers:
> I used amber package to do a protein simulation with amber99 forcefield.
> According to the reference charpter of amber9 manual ff99 should be
>referened by J. Comput. Chem. 21, 1049-1074 (2000).
> On the other hand, protein simulation forcefield should be referened by
>Adv. Prot. Chem.66, 27-85 (2003).
> I am confusing. which reference shoud be citated? thanks for any advice.
> best regards.
> caoch
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Received on Sun Jan 07 2007 - 06:07:22 PST
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