[gmx-users] Release of R.E.D. Server

FyD fyd at q4md-forcefieldtools.org
Thu Apr 9 10:31:30 CEST 2009

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 http://q4md-forcefieldtools.org/REDS/faq.php 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 q4md-fft at q4md-forcefieldtools.org  
after registration at sympa at q4md-forcefieldtools.org. 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  
http://q4md-forcefieldtools.org/RED/, the RESP ESP charge DDataBase  
(or R.E.DD.B. http://q4md-forcefieldtools.org/REDDB/) 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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