Dear All, I am pleased to announce the release of R.E.D. Server 2.0. See http://q4md-forcefieldtools.org/REDS/.
R.E.D. Server is a web service designed to automatically derive RESP and ESP charges, and to build force field libraries for new molecules/molecular fragments. R.E.D. Server provides to computational biologists involved in AMBER, CHARMM, GLYCAM & OPLS force field based biological studies the software and hardware required for charge derivation and force field library building. See http://q4md-forcefieldtools.org/REDS/faq.php & http://q4md-forcefieldtools.org/REDS/news.php A cluster of quadri-core Intel Xeon and AMD dual-Core Opteron is the machine on which R.E.D. Server is installed and where calculations are performed. R.E.D. Server uses Apache, Torque, Maui as well as OpenMPI under CentOS 5.4. R.E.D. Server 2.0 is open to all users and registration to interact with R.E.D. Server is not mandatory. The source code of R.E.D. Server 2.0 is distributed under the GNU general public license allowing any user to create her/his own R.E.D. Server. Consequently, the licenses signed by the users of R.E.D. Server 1.0 are not valid anymore. In agreement with the developers of GAMESS, Firefly and Gaussian Inc., R.E.D. Server provides the latest version of the GAMESS, Firefly and Gaussian binaries: See http://q4md-forcefieldtools.org/REDS/faq.php#3 for the conditions of use of R.E.D. Server 2.0. A standalone version of the RESP program is also interfaced: See http://q4md-forcefieldtools.org/RED/resp/ R.E.D. Server 2.0 executes the latest version of the Ante_R.E.D. 2.0 and R.E.D. IV versions developed by the q4md force field tools team. New features developed in Ante_R.E.D. 2.0 are: - the resolution of molecular topology (with reconstruction of the topology for bad input geometries), - the determination of rigorous chemical equivalencing (used in charge equivalencing), - the development of various approaches for atom reordering as well as - the definition of atom names and residue name(s) (i. e. two atoms in a residue belonging to a force field library cannot share the same name). See http://q4md-forcefieldtools.org/REDS/news.php#2 R.E.D. presents the following features: - compatibility with UNIX, MacOS and Windows operating systems - RESP and ESP charge derivation for whole molecules and molecular fragments - building of force field libraries for whole molecules and potentially for any type of molecular fragments - highly reproducible charge values independently of the QM programs or initial structures selected - use of multiple orientations, multiple conformations and/or multiple molecules in RESP and ESP charge derivation - modular approach allowing the development of new approaches/adaptations - chemical elements up to Bromine automatically handled. See http://www.ncbi.nlm.nih.gov/pubmed/20574571 NIHMSID: NIHMS215785 R.E.D. IV June 2010 presents many new features as well. This includes: - the reinforcement of charge reproducibility, - the recalculation of Cartesian coordinates for molecular fragments originating from the fusion between two molecules, - the building of complex force field topology databases for any type of bio-organic and bio-inorganic molecules, - the generation of all-atom force field libraries or united-carbon force field libraries - the development of a statistic module allowing charge value comparisons (i. e. a first attempt for validating charge values). See http://q4md-forcefieldtools.org/REDS/news.php#IV Help for R.E.D. Server users is provided through a private assistance system or a public mailing list. See http://q4md-forcefieldtools.org/REDS/help-log.php & http://lists.q4md-forcefieldtools.org/wws/info/q4md-fft A demonstration is also available from the Demo service. http://q4md-forcefieldtools.org/REDS/RED-Server-demo1.php A tutorial is available and it has been updated according to the new features implemented in R.E.D. Server 2.0. See http://q4md-forcefieldtools.org/Tutorial.php Data generated using R.E.D. Server might be automatically submitted to R.E.DD.B. if one wants to use this option. See http://q4md-forcefieldtools.org/REDDB/ & http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238896/ For each project computed by R.E.D. Server a Jmol based graphical interface is also generated allowing the user studying and displaying the corresponding data. See screenshots: http://q4md-forcefieldtools.org/REDS/images/Screenshot1.gif http://q4md-forcefieldtools.org/REDS/images/Screenshot2.gif http://q4md-forcefieldtools.org/REDS/images/Screenshot3.gif We are grateful to Alineos SA http://www.alineos.com/ for supporting this project. regards, Francois F.-Y. Dupradeau --- http://q4md-forcefieldtools.org/FyD/ ------------------------------------------------------------------------------ Increase Visibility of Your 3D Game App & Earn a Chance To Win $500! 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