From owner-chemistry*- at -*ccl.net Sun Aug 28 22:27:37 2005
From: "CCL" <owner-chemistry]-[server.ccl.net>
To: CCL
Subject: Re: CCL: Release of R.E.D-II
X-Original-From: LI Daobing <lidaobing]-[gmail.com>
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Date: Mon, 11 Jul 2005 13:46:28 +0800
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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