From owner-chemistry@ccl.net Thu Apr 9 06:09:00 2009 From: "FyD fyd%q4md-forcefieldtools.org" To: CCL Subject: CCL:G: Release of R.E.D. Server Message-Id: <-39043-090409052606-30202-dRlXl89DXBtL303uPW76oA%%server.ccl.net> X-Original-From: FyD Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Thu, 09 Apr 2009 10:31:30 +0200 MIME-Version: 1.0 Sent to CCL by: FyD [fyd]*[q4md-forcefieldtools.org] Dear All, I am pleased to announce the release of R.E.D. Server available * =20 http://q4md-forcefieldtools.org/REDS/. R.E.D. Server provides the software and hardware (i. e. a cluster of =20 computers) required for the derivation of highly effective and =20 reproducible RESP and ESP atomic charge values embedded in force field =20 libraries suitable for molecular dynamics simulations. R.E.D. Server =20 interfaces the last stable version of the RESP ESP charge Derive =20 program (R.E.D. IV April 2009 so far) developed by the q4md force =20 field tools team, and provides the binaries for the last versions of =20 the Gaussian, GAMESS-US, or the PC-GAMESS/Firefly program, and for the =20 RESP program. More generally, the last developments in term of RESP =20 and ESP charge derivation carried out by the q4md force field tools =20 team will be provided through R.E.D. Server. The release of these new =20 developments will be carried out from time to time, and the =20 description of those last features released in R.E.D. Server is =20 available at the "R.E.D. Server news" web page. By involving multiple molecules, multiple conformations and multiple =20 orientations in charge derivation and by handling specific charge =20 constraints during the fitting step, R.E.D. IV allows building complex =20 force field topology database or FFTopDB corresponding to the =20 simultaneous generation of numerous molecular fragments (N-terminal, =20 C-terminal and central amino acid fragments, 5'- or Y'-terminal, 3'- =20 or X'-terminal and central nucleotide fragments as well as =20 monosaccharide and metal complex fragments) in a single execution. The =20 all atom or united-carbon force field library model can be =20 in-differentially generated. A procedure to study the impact of the =20 various charge constraints required during the fitting step of a =20 molecular fragment has been implemented allowing users to compare =20 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 =20 Asked Questions http://q4md-forcefieldtools.org/REDS/faq.php as well =20 as in a specific tutorial =20 http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php. Academic users involved in non-profit research are authorized to use =20 R.E.D. Server. The use of R.E.D. Server is provided at no cost after =20 signing a license agreement. The PI (principal investigator or =20 Director of a laboratory) and the PU (R.E.D. Server principal user) =20 have to register and sign a license agreement to be authorized to use =20 R.E.D. Server. A general public help is provided with the q4md-forcefieldtools =20 mailing list. Any researcher can participate in this mailing list by =20 answering and/or sending queries at q4md-fft*q4md-forcefieldtools.org =20 after registration at sympa*q4md-forcefieldtools.org. Archives of the =20 q4md-fft mailing list are public. A private assistance is also =20 available for registered users from the "Assistance" Service available =20 at the R.E.D. Server Home page. We are registered in the AMBER and CCL =20 mailing lists, and we will answer to the queries about the q4md force =20 field tools in these mailing lists as well. The R.E.D. III.2 tools distributed in a standalone version at =20 http://q4md-forcefieldtools.org/RED/, the RESP ESP charge DDataBase =20 (or R.E.DD.B. http://q4md-forcefieldtools.org/REDDB/) which allows =20 freely storing and distributing RESP and ESP charges embedded in force =20 field libraries in the scientific community and R.E.D. Server =20 constitute to the best of our knowledge unique tools. regards, F.-Y. Dupradeau --- http://q4md-forcefieldtools.org/FyD/