From chemistry-request@ccl.net Sat Jul 9 23:54:57 2005 Received: from mx1.ustc.edu.cn (ns.ustc.edu.cn [202.38.64.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j6A3srlO010542 for ; Sat, 9 Jul 2005 23:54:55 -0400 Received: from dxl ([210.45.66.65]) by mx1.ustc.edu.cn (8.11.6/8.11.6) with SMTP id j6A3off13545; Sun, 10 Jul 2005 11:50:41 +0800 Message-Id: <200507100350.j6A3off13545^at^mx1.ustc.edu.cn> Date: Sun, 10 Jul 2005 11:56:24 +0800 From: "Ding Xunlei" Reply-To: dxl^at^ustc.edu.cn To: "molpro-user" , "chemistry" Subject: EA calculation in molpro Organization: University of Science and Technology of China X-mailer: Foxmail 5.0 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="gb2312" X-Spam-Status: No, score=1.8 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_WHOIS,MIME_BASE64_BLANKS,MIME_BASE64_TEXT autolearn=no version=3.0.4 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id j6A3svlO010593 Dear All#: How to calculate EA in molpro with CASSCF method? I want to calculate the EA of O2 using the input file below. But the result is: OPTG CASSCF HF-SCF OPTG CASSCF HF-SCF -149.70622861 -149.68659926 -149.63128302 -149.75931902 -149.75928830 -149.65358218 The energy of O2- is higher than O2. What's wrong ? ***,O2 geometry={O1; O2,O1,R } R=1.213 ang basis={ spdf,o,avtz;c; } hf wf, 16, 4, 2 casscf optg hf wf, 17, 6, 1 casscf optg --- Thank you for your help! Yours sincerely, Ding Xunlei 2005-07-10 ______________________________________________ From chemistry-request@ccl.net Sun Jul 10 02:13:32 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j6A6DWi4002128 for ; Sun, 10 Jul 2005 02:13:32 -0400 Received: from 66.93.212.3 (SquirrelMail authenticated user jkl) by server.ccl.net with HTTP; Sun, 10 Jul 2005 02:13:32 -0400 (EDT) Message-ID: <54398.66.93.212.3.1120976012.squirrel..at..server.ccl.net> Date: Sun, 10 Jul 2005 02:13:32 -0400 (EDT) Subject: Changes in CCL distribution From: jkl..at..ccl.net To: chemistry..at..ccl.net User-Agent: SquirrelMail/1.4.4-1.FC3 MIME-Version: 1.0 Content-Type: text/plain;charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) Importance: Normal X-Spam-Status: No, score=-2.6 required=5.0 tests=ALL_TRUSTED,NO_REAL_NAME autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Dear CCL, As some of you know, the CCL runs from my home for a few months. So, there are nobody around to do CCL chores when I am in travel Since I am taking off for Europe for five weeks on the 11th, we have a problem: A) If one of the key computers dies, there is nobody around to push the button or fix it (e.g., replace the disk from backup). This is quite a real possibility, since it is hot here, and the thunderstorms in Ohio are frequent and intense. B) I will be visiting 4 countries, and I also plan to shed some fat hiking, i.e., I may only be occasionally on the Internet. CCL gets about 3000 spam messages a day. Moreover, the attacks are getting quite annoying. For example, the crackers place viruses on your Windows computers. Those boxes send messages with viruses and/or spam with the chemistry..at..ccl.net on the From: line. On the To: line, they place some random addresses from your address book, or from internal virus cache. The target machines bounce this junk mail to the CCL. Since the bounce comes from the legitimate machine, the blacklists do not work. BTW, educate your system administrators that bouncing mail that they consider a spam or virus to a header or envelope From address does not make any sense. In 99% of cases spam/virus do not provide a real addresses of the sender. To keep the CCL running, I had to make dramatic changes in its distribution. I will replace current scripts to reflect a new mode of distribution (I am still testing them, and my wife tells me that I should pack...). We will be debugging the stuff as we go. Sorry... (Some of you know that I am very busy lately). The main changes will be: 1) The address of the original author of the message does not appear on the From: line of the CCL message. The From: line and envelope MAIL FROM will be always coming from: owner-chemistry..at..server.ccl.net. Obfuscated (i.e., with the @ sign replaced by RANDOM strange characters) author's address will still be available on the X-Original-From: header line and as the first line of the message body. If you want to reply to the author, you need to cut/paste and then edit his/her address manually. Why: a) so your infected/zombified computers do not collect addresses automatically. b) so the bouncing mail from your defunct computers or defunct e-mail addresses can be processed automatically by the script collecting mail at owner-chemistry address. c) to make it not cost effective for the malware that resides on your computer to collect e-mail addresses from your mailbox (Do not say that you do not have spyware on your Windows, you just do not know about it...). 2) When you send an e-mail message to chemistry..at..ccl.net or use the web form to post message to CCL forum, you will get back the request for confirmation. This step is necessary, since faking the From: address on the e-mail is trivial, and due to spammers, well over half of the mail on the Internet does not have a true e-mail address. Those of you who posted to CCL via the web form are already familiar with the confirmations. You can either confirm your message via Web link provided in the confirmation request, or by replying to the confirmation message. When you use replay, please do not edit/change the message in any way. 3) After CCL gets the confirmation from you, the message will be posted to subscribers only if you posted to CCL before from the same address. If this is the first post from your address, your message will be held until human (me) releases it to the list. As you know, the beauty (and challenge) of CCL is that you do not have to be subscribed to CCL to post to it. You can view messages at: http://www.ccl.net/chemistry/resources/messages/index.shtml and submit messages via Web form at: http://www.ccl.net/cgi-bin/ccl/send_ccl_message The only way to ordain you to be the bona fide uncensored poster is that you post something sensible to CCL successfully. If you post something that violates CCL rules: http://www.ccl.net/chemistry/aboutccl/rules/ you will be removed from the blessed contributors list very soon {:-(} 4) Each CCL message will be sent individually to every subscriber, i.e., the e-mail address and name with which you are subscribed to CCL will appear on the To: header line of CCL message (I am sure that some long-timers will be surprised what they see there). Moreover, the To: (and the Message-Id:) line will contain a "secret" {:-)} code that will allow you to unsubscribe via Web or by sending e-mail to a special address without human intervention. It will also allow the scripts to unsubscribe you automatically when the mail starts bouncing from your e-mail address. This is still under development... 5) Attachments with MIME application/ANYTHING will not be posted. Please do not sign your messages (you will not be on the From line anyhow), do not attach beloved MS-WORD files and PostScript, etc... There are scores of exploits in different applications, and I just cannot take a risk. All the malware checkers by definition play the catch-up game, and the jerks are always ahead. 6) If something if found wrong with your message (or perceived wrong by my buggy perl scripts), you will not get any answers. I do not want to flood innocent people with messages in case someone wants to crack my software. In other words, the filters will DROP, not REJECT. But I will constantly study what is happening. Bug me if your message does not appear on the list. In short... Expect the unexpected... Otherwise, the CCL would have to take vacations, but you probably do not want this. I hope we will not experience any irresponsible posts on CCL. If we do, however, these messages will not be anonymous (the message cannot be posted unless you confirm that you are you), and therefore, the abusers cannot hide (unless they brake into someone's computer, including mine). If this becomes a problem, I will keep plugging the holes. One more thing... I am getting scores of bounces that do not like this or that in the CCL message at random times for wrong reasons [false positives in spam filters]. For example: "Nobody speak Chinese here", or "Too many messages today", etc. Please whitelist the CCL... I do not remember when the spam message was last posted on the CCL. You do not risk much, especially with application MIMEs forbidden on the list. If something goes very wrong, I will allow some people to issue the "shutdown" command when I am not around. But then, the lights will go down until I come back. I do not have the network wake-up installed yet on the boxes that run CCL, though I plan to do it one day. Expect many improvements when I return from my travels, though it will take some time. I hope to have more time to spend on CCL with your help and I will try to update/restore many services that used to run on CCL, but that had to be disabled or neglected since I still need to sleep at least 5 hours a day on average... All the best and have fun, even if it is hard to be worry free in these brutal world... Your CCL serviceman Jan K. Labanowski jkl..at..ccl.net From chemistry-request@ccl.net Sun Jul 10 03:48:11 2005 Received: from mout2.freenet.de (mout2.freenet.de [194.97.50.155]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j6A7m6vP019991 for ; Sun, 10 Jul 2005 03:48:06 -0400 Received: from [194.97.50.138] (helo=mx0.freenet.de) by mout2.freenet.de with esmtpa (Exim 4.52) id 1DrVrv-00016H-UY for chemistry * ccl.net; Sun, 10 Jul 2005 09:04:51 +0200 Received: from j12d0.j.pppool.de ([85.74.18.208]) by mx0.freenet.de with esmtpa (ID rudnyi * freenet.de) (Exim 4.52 #3) id 1DrVrv-0007PK-LX for chemistry * ccl.net; Sun, 10 Jul 2005 09:04:51 +0200 Message-ID: <42D0C892.7030107 * imtek.uni-freiburg.de> Date: Sun, 10 Jul 2005 09:04:50 +0200 From: Evgenii Rudnyi User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry * ccl.net Subject: CCL: ATLAS and BLAS libraries for dual-core CPUs References: <42D04ABC.9050305 * attglobal.net> In-Reply-To: <42D04ABC.9050305 * attglobal.net> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Warning: 85.74.18.208 is listed at list.dsbl.org X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net > Where might I find info on BLAS and ATLAS libraries for INTEL and AMD > dual-core CPUs, and Windows and Linux OSs? Everything that concerns ATLAS is at http://math-atlas.sourceforge.net/ ATLAS libraries is the optimized BLAS so you do not need both. ATLAS can do multithreading indeed. If you do not find a prebuilt library at the site above, just compile it > from the code. It takes some time but it is fun. Just follow docs. Best wishes, Evgenii Rudnyi -- IMTEK-Institute for Microsystem Technology Simulation of Microsystems Freiburg University Georges-Koehler-Allee 103 D-79110 Freiburg i. Br. Germany Tel. (+49 761) 203 7383 Fax (+49 761) 203 7437 http://www.imtek.uni-freiburg.de/simulation/mor4ansys/ http://Evgenii.Rudnyi.Ru/ From chemistry-request@ccl.net Sun Jul 10 12:05:52 2005 Received: from web52014.mail.yahoo.com (web52014.mail.yahoo.com [206.190.48.97]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j6AG5mYd030171 for ; Sun, 10 Jul 2005 12:05:48 -0400 Received: (qmail 38026 invoked by uid 60001); 10 Jul 2005 15:05:46 -0000 DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=Message-ID:Received:Date:From:Subject:To:In-Reply-To:MIME-Version:Content-Type:Content-Transfer-Encoding; b=fMwviTRDJ9nCpKE0hta6vzFTzdV8J3yMWB/kuz3+ObKheIWWEWdjICT8QmzUR2Gl73nbJOvV8Qzt6vNTFabDMOLLZLKHE/Bm2ke0Wc13TEmipIzPbk/kCchvkdA4Wd2qm/jkd2v+qf2s4WLwAEf/S+MpH9xJJ27HHvGM3dGoKDA= ; Message-ID: <20050710150546.38024.qmail (a) web52014.mail.yahoo.com> Received: from [4.239.219.141] by web52014.mail.yahoo.com via HTTP; Sun, 10 Jul 2005 08:05:46 PDT Date: Sun, 10 Jul 2005 08:05:46 -0700 (PDT) From: Konstantin Kudin Subject: Re: CCL: ATLAS and BLAS libraries for dual-core CPUs To: chemistry (a) ccl.net In-Reply-To: <42D0C892.7030107 (a) imtek.uni-freiburg.de> MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net There is even a better alternative to Atlas' implementation of BLAS. The GOTO library containing hand optimized assembler is nothing short of spectacular in terms of performance: http://www.cs.utexas.edu/users/flame/goto/ Kostya --- Evgenii Rudnyi wrote: > > Where might I find info on BLAS and ATLAS libraries for INTEL and > AMD > > dual-core CPUs, and Windows and Linux OSs? > > Everything that concerns ATLAS is at > > http://math-atlas.sourceforge.net/ > > ATLAS libraries is the optimized BLAS so you do not need both. > > ATLAS can do multithreading indeed. > > If you do not find a prebuilt library at the site above, just compile > it > > from the code. It takes some time but it is fun. Just follow docs. > > Best wishes, > > Evgenii Rudnyi > -- > IMTEK-Institute for Microsystem Technology > Simulation of Microsystems > Freiburg University > Georges-Koehler-Allee 103 > D-79110 Freiburg i. Br. > Germany > Tel. (+49 761) 203 7383 > Fax (+49 761) 203 7437 > http://www.imtek.uni-freiburg.de/simulation/mor4ansys/ > http://Evgenii.Rudnyi.Ru/ > > -= This is automatically added to each message by the mailing script > =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line > and send your message to: CHEMISTRY (a) ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST (a) ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, > please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > ____________________________________________________ Sell on Yahoo! Auctions no fees. Bid on great items. http://auctions.yahoo.com/ From owner-chemistry@ccl.net Sun Jul 10 15:07:42 2005 From: "CCL" To: CCL Subject: CCL: Test on Jul 10, 1:01pm/Testing code removal / Testing code removal / Testing code removal Message-Id: <-28859-050710134821-4182-uNy46x+EILo1kNckC1/Z/g^-^server.ccl.net> X-Original-From: Jan K Labanowski Sent to CCL by: Jan K Labanowski Testing code removal -- Jan K. Labanowski, Ph.D. Tel. (574) 631-5465 Science Computing Facility FAX (574) 631-9293 University of Notre Dame 225 Nieuwland Science Hall Notre Dame, IN 46556-5670 ----- Forwarded message from CCL ----- Date: Sun, 10 Jul 2005 13:07:00 -0400 From: CCL Reply-To: CCL Subject: CCL: Test on Jul 10, 1:01pm To: "Labanowski, Jan " Sent to CCL by: Jan K Labanowski Test on Jul 10, 1:01pm -- Jan K. Labanowski, Ph.D. Tel. (574) 631-5465 Science Computing Facility FAX (574) 631-9293 University of Notre Dame 225 Nieuwland Science Hall Notre Dame, IN 46556-5670----- End forwarded message ----- From chemistry-request@ccl.net Sun Jul 10 16:00:05 2005 Received: from sims.csuohio.edu (csu-137-148-5-58.csuohio.edu [137.148.5.58]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j6AK04Hx012158 for ; Sun, 10 Jul 2005 16:00:04 -0400 Received: from csu-mail0 (sims [137.148.5.32]) by sims.csuohio.edu (Sun Internet Mail Server sims.4.0.1999.09.28.17.31.p2) with ESMTP id <0IJF00C2J6K5NY:at:sims.csuohio.edu> for CHEMISTRY:at:ccl.net; Sun, 10 Jul 2005 12:16:53 -0400 (EDT) Date: Sun, 10 Jul 2005 12:16:53 -0400 (EDT) From: d.dogaru+csuohio.edu:at:sims.csuohio.edu Subject: CCL: Electron Transfer To: CHEMISTRY:at:ccl.net Message-id: <496992315.1121012213630.JavaMail.root@csu-mail0> MIME-version: 1.0 X-Mailer: Sun(TM) Web Access 1.2 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 7BIT X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME autolearn=no version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Hello, I would exceedingly appreciate if someone were as kind as to direct me to software that is capable of performing electron transfer pathway calculations in enzymes. As it were, I have observed several references [in certain papers] regarding such a program [-- capable of performing electron transfer pathway calculations in enzymes--] i.e., GreenPath software, but I was unable to find the program! Thanks, Daniela From owner-chemistry@ccl.net Sun Jul 10 17:10:14 2005 From: "CCL" To: CCL Subject: CCL: This is another test Message-Id: <-28860-050710170903-16649-uNy46x+EILo1kNckC1/Z/g!A!server.ccl.net> X-Original-From: Jan K Labanowski Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 MIME-Version: 1.0 Sent to CCL by: Jan K Labanowski -- Jan K. Labanowski, Ph.D. Tel. (574) 631-5465 Science Computing Facility FAX (574) 631-9293 University of Notre Dame 225 Nieuwland Science Hall Notre Dame, IN 46556-5670 From owner-chemistry@ccl.net Sun Jul 10 20:07:20 2005 From: "CCL" To: CCL Subject: CCL: Testing new CCL scripts, please delete Message-Id: <-28861-050710195132-26124-uNy46x+EILo1kNckC1/Z/g(-)server.ccl.net> X-Original-From: Jan K Labanowski Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 MIME-Version: 1.0 Sent to CCL by: Jan K Labanowski Dear CCL, I am sorry but I need to test the new scripts. Please delete this message, and be patient with me... Jan -- Jan K. Labanowski jkl(-)ccl.net From owner-chemistry@ccl.net Sun Jul 10 21:46:20 2005 From: "CCL" To: CCL Subject: CCL: Release of R.E.D-II Message-Id: <-28862-050710202736-28038-uNy46x+EILo1kNckC1/Z/g|"|server.ccl.net> X-Original-From: gurusamy gurusamy Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1325370518-1121041650=:67588" MIME-Version: 1.0 Sent to CCL by: gurusamy gurusamy --0-1325370518-1121041650=:67588 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit dear sir do you have tutorial for running MD lipid bilayers pg FyD 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.htmMr. 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. --0-1325370518-1121041650=:67588 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
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. --0-1325370518-1121041650=:67588-- From owner-chemistry@ccl.net Sun Jul 10 21:50:13 2005 From: "CCL" To: CCL Subject: CCL: Release of R.E.D-II Message-Id: <-28863-050710202736-28038-WmjhO1gXdqcNI6R0gik6bw###server.ccl.net> X-Original-From: gurusamy gurusamy Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1325370518-1121041650=:67588" MIME-Version: 1.0 Sent to CCL by: gurusamy gurusamy --0-1325370518-1121041650=:67588 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit dear sir do you have tutorial for running MD lipid bilayers pg FyD 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.htmMr. 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. --0-1325370518-1121041650=:67588 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
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. --0-1325370518-1121041650=:67588--