Re: CCL: Release of R.E.D-II

[LI Daobing <lidaobing]-[gmail.com>]

 Sent to CCL by: LI Daobing [lidaobing]-[gmail.com]
 Try this:
 http://www.gromacs.org/documentation/tutorial.php
 On 7/11/05, CCL <owner-chemistry]-[ccl.net> wrote:
 > dear sir
 > do you have tutorial for running MD lipid bilayers
 > pg
 >
 > FyD <fyd]-[u-picardie.fr> wrote:
 > Dear All,
 >
 > I am pleased to announce the release of the R.E.D. program, version 2.0.,
 > http://www.u-picardie.fr/labo/lbpd/RED/.
 >
 > 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
 > R.E.D.
 >
 > - A new manual has been written taking into account most of the problems
 > discussed in the AMBER mailing list.
 > See http://www.u-picardie.fr/labo/lbpd/RED/RED-II.pdf
 >
 > - The FAQ about R.E.D. I has been updated, and contains now more than 50
 > FAQs.
 > See http://www.u-picardie.fr/labo/lbpd/RED/FAQ-I.htm
 > - The FAQ about R.E.D II will be updated and is be available at:
 > http://www.u-picardie.fr/labo/lbpd/RED/FAQ-II.htm
 >
 > - The six bugs reported for R.E.D. I,
 > http://www.u-picardie.fr/labo/lbpd/RED/bugs-I, have been
 > corrected.
 > - The future bugfixes for the R.E.D. II bugs will be available at
 > http://www.u-picardie.fr/labo/lbpd/RED/bugs-II
 >
 > - The X R.E.D. graphical interface,
 > http://www.u-picardie.fr/labo/lbpd/RED/XRED.htm, 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
 > --
 > http://www.u-picardie.fr/labo/lbpd/FyD.htm
 >
 >
 >
 >
 >
 >
 >
 >
 >
 >
 >
 > Mr. P. Gurusamy,
 > Lecturer in Chemistry (S.G),
 > Department of Chemistry,
 > Sri. Ramasay Naidu Memorial College,
 > Sattur-626203,
 > Virudhunagar District,
 > Tamilnadu,
 > India.
 >
 >  ________________________________
 >  Sell on Yahoo! Auctions - No fees. Bid on great items.
 >
 >
 --
 LI Daobing