AMBER: Release of R.E.D-II

From: FyD <>
Date: Thu, 07 Jul 2005 19:58:54 +0200

Dear All,

I am pleased to announce the release of the R.E.D. program, version 2.0.,

We developed the R.E.D. I program (RESP ESP charge Derive, version 1.0) to
automatically derive 'RESP' and 'ESP' charges starting from an un-optimized PDB
structure. R.E.D. sequentially executes (i) either the "GAMESS" program or the
"Gaussian" program to optimize the target structure and to compute the
corresponding MEP, and (ii) the "RESP" program to fit the atom-centered charges
to the grid previously determined. Format conversions needed during the
procedure and "GAMESS", "Gaussian" and "RESP" inputs are automatically
generated by R.E.D. By controlling the molecular orientation of the optimized
geometry, a new RESP fitting procedure based on multi-orientation feature is
proposed and allows getting highly reproducible 'RESP' and 'ESP' charges
whatever the QM software and starting Cartesian coordinates are.

With R.E.D. II (version 2.0), multi-conformation RESP and ESP fit has been
implemented, and can also be automatically carried out using a well defined set
of molecular conformations. Thus, 'multi-conformation' and 'multi-orientation'
RESP fit can be performed together or independently according to the user
choice. 'Standard' but also 'non-standard' RESP inputs can now be generated.
The geometry optimization ouput generated by one of the two QM programs can be
used as input for MEP computation using the second QM program. Finally, RESP
and ESP charges can be derived for chemical elements having up to a total
number of electrons, Z = 35. And much more...

Thus, R.E.D. makes the derivation of the 'RESP' and 'ESP' charges a
straightforward, simple and highly reliable procedure.

R.E.D. has been written with the "Perl" programming language, and X R.E.D. with
the "tcl/tk" programming language, making these two programs highly flexible
and portable. R.E.D. and X R.E.D. have been tested on PC-LINUX and SGI-IRIX
workstations, but should work on all other UNIX platforms. They are "free" (i.
e. provided at no cost) for academic users after signing a license. On the
contrary, a fee is demanded to commercial users for the use of R.E.D. & X

- A new manual has been written taking into account most of the problems
discussed in the AMBER mailing list.

- The FAQ about R.E.D. I has been updated, and contains now more than 50 FAQs.
- The FAQ about R.E.D II will be updated and is be available at:

- The six bugs reported for R.E.D. I,, have been corrected.
- The future bugfixes for the R.E.D. II bugs will be available at

- The X R.E.D. graphical interface,, has been updated to execute
R.E.D. II.

- Finally, all the users which used a R.E.D.-II beta version, should re-download
R.E.D.-II since new features have just been added in the final version.

Best regards, Francois

  F.-Y. Dupradeau
DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
The Scripps Research Institute, La Jolla, CA, USA
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Received on Thu Jul 07 2005 - 19:53:00 PDT
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