From: M. L. Dodson <>
Date: Mon, 15 Dec 2008 15:36:08 -0600

On Mon, Dec 15, 2008 at 09:41:24PM +0100, FyD wrote:
> 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
> ago:
> 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.

Actually, I prefer the BSD license (described by people from Berkeley
as copy center: take it down to the copy center and make all the
copies you want).

> -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
> points:

No excuse is needed.

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

Obviously, since I use it I have no problem with the Amber license,
nor do I have a problem with the R.E.D. license

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

That's good.

> * 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 ;-)

I did not imply any value judgements. Not better or worse (i.e.,
black or white), just different.

HOWEVER, I would be very disappointed if R.E.D. became the STANDARD
way of generating new residue descriptions (e.g., as a replacement for
antechamber). That is what I was mainly speaking against. My view is
that "for cost" software OFFICIALLY SANCTIONED to go along with Amber
should be included in Amber, not be an additional cost burden on very
small for profit research enterprises. Big Pharma can look out for
themselves. Just as life is neither black nor white, but only grey,
not all people doing molecular dynamics fit into a university faculty
description (some of us are retired) or work in a big Pharma

> regards, Francois

And regards to you.

Bud Dodson
M. L. Dodson
Business Email: activesitedynamics-at-comcast-dot-net
Personal Email:	mldodson-at-comcast-dot-net
Phone:	eight_three_two-56_three-386_one
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Received on Wed Dec 17 2008 - 01:13:04 PST
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