AMBER Archive (2009)

Subject: [AMBER] Release of R.E.D. Server

From: FyD (
Date: Thu Apr 09 2009 - 03:31:30 CDT

Dear All,

I am pleased to announce the release of R.E.D. Server available @

R.E.D. Server provides the software and hardware (i. e. a cluster of
computers) required for the derivation of highly effective and
reproducible RESP and ESP atomic charge values embedded in force field
libraries suitable for molecular dynamics simulations. R.E.D. Server
interfaces the last stable version of the RESP ESP charge Derive
program (R.E.D. IV April 2009 so far) developed by the q4md force
field tools team, and provides the binaries for the last versions of
the Gaussian, GAMESS-US, or the PC-GAMESS/Firefly program, and for the
RESP program. More generally, the last developments in term of RESP
and ESP charge derivation carried out by the q4md force field tools
team will be provided through R.E.D. Server. The release of these new
developments will be carried out from time to time, and the
description of those last features released in R.E.D. Server is
available at the "R.E.D. Server news" web page.

By involving multiple molecules, multiple conformations and multiple
orientations in charge derivation and by handling specific charge
constraints during the fitting step, R.E.D. IV allows building complex
force field topology database or FFTopDB corresponding to the
simultaneous generation of numerous molecular fragments (N-terminal,
C-terminal and central amino acid fragments, 5'- or Y'-terminal, 3'-
or X'-terminal and central nucleotide fragments as well as
monosaccharide and metal complex fragments) in a single execution. The
all atom or united-carbon force field library model can be
in-differentially generated. A procedure to study the impact of the
various charge constraints required during the fitting step of a
molecular fragment has been implemented allowing users to compare
charge values, and thus to validate or reject charge sets.

The use of R.E.D. Server and R.E.D. IV is described in Frequently
Asked Questions as well
as in a specific tutorial

Academic users involved in non-profit research are authorized to use
R.E.D. Server. The use of R.E.D. Server is provided at no cost after
signing a license agreement. The PI (principal investigator or
Director of a laboratory) and the PU (R.E.D. Server principal user)
have to register and sign a license agreement to be authorized to use
R.E.D. Server.

A general public help is provided with the q4md-forcefieldtools
mailing list. Any researcher can participate in this mailing list by
answering and/or sending queries at
after registration at Archives of the
q4md-fft mailing list are public. A private assistance is also
available for registered users from the "Assistance" Service available
at the R.E.D. Server Home page. We are registered in the AMBER and CCL
mailing lists, and we will answer to the queries about the q4md force
field tools in these mailing lists as well.

The R.E.D. III.2 tools distributed in a standalone version at, the RESP ESP charge DDataBase
(or R.E.DD.B. which allows
freely storing and distributing RESP and ESP charges embedded in force
field libraries in the scientific community and R.E.D. Server
constitute to the best of our knowledge unique tools.


            F.-Y. Dupradeau

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