AMBER Archive (2008)


From: FyD (
Date: Mon Dec 15 2008 - 14:41:24 CST

Dear Dr Dodson,

> I think the R.E.D. license is completely incompatible with the
> AmberTools license. Of course, people who write software have the
> complete right to put whatever license they wish on their work
> product, so I am not complaining about that. I just think the
> AmberTools project is in the best tradition of academic research and
> would like to see it promoted, but R.E.D., based on its license, is
> not working toward the same end. In my opinion, of course.

-1- I totally agree with you, here! The actual R.E.D. license is
indeed not compatible with the AmberTools. I am particularly sensible
to this problem. The best proof is the paper we have written some time
F.-Y. Dupradeau & J. Rochette, Bugs in Computational Chemistry
Software & their Consequences: The Importance of the Source Code, J.
Mol. Model., 2003, 9, 271-272.

-2- When you say "the AmberTools project is in the best tradition of
academic research", I also 100 % agree with you; i.e. I really think
the GPL license is great. GNU is a really beautiful idea.

-3- That being said, I do not want to find any excuse for the actual
license of the R.E.D. tools, but I would like to remind you several

* The R.E.D. tools are written in perl & tcl/tk. The sources are
consequently provided.

* The AmberTools became "GNU" just recently. Before, they were
copyrighted similarly as the R.E.D. tools are nowadays. Everybody can

* Sander is still copyrighted & is not GNU, while Gromacs is GNU for instance.
Amber10 is still sold to academics.

* Projects in R.E.DD.B. are free in sense of freedom for download.

* Our two teams are small: We are trying to sell the R.E.D. tools to
private companies to get some money to re-invest in research. By this
way, we were able to pay for instance the open-source access of our
R.E.DD.B. paper in Nucl. Acids Res.

So please, life is neither black nor white, but only grey ;-)

regards, Francois

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