From chemistry-request@ccl.net Thu May 26 05:03:41 2005 Received: from mailgateway1.uni-freiburg.de (mailgateway1.uni-freiburg.de [132.230.2.211]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4Q93bWj032392 for ; Thu, 26 May 2005 05:03:38 -0400 Delivery-date: Thu, 26 May 2005 11:03:37 +0200 Received: from waugh.imtek.uni-freiburg.de ([132.230.168.49]) port 52837 by mailgateway1.uni-freiburg.de with esmtp (Exim 4.50 #1 built 18-Feb-2005 14:34:25 running on Gentoo) id 1DbDVu-0003Nz-9A for chemistry !! ccl.net; Thu, 26 May 2005 10:14:46 +0200 Mime-Version: 1.0 (Apple Message framework v622) Content-Transfer-Encoding: 7bit Message-Id: <463e4194a74a8cfc5ab17b82147de40a !! imtek.uni-freiburg.de> Content-Type: text/plain; charset=US-ASCII; format=flowed To: chemistry !! ccl.net From: Evgenii Rudnyi Subject: CCL: course Molecular Simulation for MST Date: Thu, 26 May 2005 10:13:19 +0200 X-Mailer: Apple Mail (2.622) X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hi, I would like to announce our course that has been developed at IMTEK: Molecular Simulation for MST Engineers. Short course description is at http://evgenii.rudnyi.ru/doc/teaching/md/MSTpreprint.pdf Lecture notes are at http://evgenii.rudnyi.ru/teaching.html#md The course is designed as introduction into molecular simulation. Best wishes, Evgenii Rudnyi -- http://Evgenii.Rudnyi.Ru/ http://www.imtek.uni-freiburg.de/simulation/ From chemistry-request@ccl.net Thu May 26 02:45:47 2005 Received: from wproxy.gmail.com (wproxy.gmail.com [64.233.184.206]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4Q6jkaO028122 for ; Thu, 26 May 2005 02:45:46 -0400 Received: by wproxy.gmail.com with SMTP id 71so1020695wra for ; Wed, 25 May 2005 23:45:45 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:cc:mime-version:content-type:content-transfer-encoding:content-disposition; b=rsm7cRVC0TV+QbYEP9FqmBchVWCldOymefRMm+R1B+gkgMvsMoPp69518NgV2BZ/G9accnhDlP2QyZ7kx8YynHyLLJQfknhTAFhJ09+m6DERV0wL6iO2TdYQ2mzkWqfxy9dOF+BLmBoNfmX/swIO30E7tWXlZeD0O0YBbpv6lpc= Received: by 10.54.145.14 with SMTP id s14mr802163wrd; Wed, 25 May 2005 22:45:44 -0700 (PDT) Received: by 10.54.22.26 with HTTP; Wed, 25 May 2005 22:45:44 -0700 (PDT) Message-ID: <2e76add90505252245359a826f = = = mail.gmail.com> Date: Thu, 26 May 2005 07:45:44 +0200 From: Szilveszter Juhos Reply-To: Szilveszter Juhos To: Lucilla angeli Subject: Re: CCL:macrocycles Cc: CCL Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Disposition: inline X-Spam-Status: No, score=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE,RCVD_BY_IP autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j4Q6jlaO028126 Dear Lucilla, Since bound ligands are usualy in a more or less relaxed conformation in the binding pocket your suggestion is valid as generating more conformations for the big rings and dock each set separatelly keeping the ring rigid (least it was what we done before :) I know it is not the optimal solution but docking software is unlikely to change the dihedrals in a ring. Also note structures with poor resolution (3-3.5 A) are not really the best for docking. If your big ligand is just sticking to the surface of the target, it will be again tough to find a correct docked conformation (regardless of ring size) . Cheers: Szilva On 5/25/05, Lucilla angeli wrote: > Dear CCLers > > I had a question about the docking of cyclic compounds, like macrocyclic > lactones or macrolides. > Does anyone know or have ever applied a computational protocol to dock > macrocycles with many degrees of freedom into a protein? > I don't know how to approach the problem.... > Perhaps a conformational analysis with Maestro and then a docking with > Autodock (that, however, is not able to take into account the > flexibility of the ring)...... > I wait hopeful for your suggestions. > > Thanks in advance > Lucilla Angeli > > > > -= 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 = = = ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST = = = 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 > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Thu May 26 00:28:10 2005 Received: from hotmail.com (bay104-f28.bay104.hotmail.com [65.54.175.38]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4Q4S6Gq023903 for ; Thu, 26 May 2005 00:28:07 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Wed, 25 May 2005 20:41:02 -0700 Message-ID: Received: from 65.54.175.206 by by104fd.bay104.hotmail.msn.com with HTTP; Thu, 26 May 2005 03:41:01 GMT X-Originating-IP: [65.54.175.206] X-Originating-Email: [liuxin_dut = = = hotmail.com] X-Sender: liuxin_dut = = = hotmail.com From: "Xin Liu" To: chemistry = = = ccl.net Subject: CCL: Electronic structure of O2 and O atom Date: Thu, 26 May 2005 03:41:01 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed X-OriginalArrivalTime: 26 May 2005 03:41:02.0192 (UTC) FILETIME=[BCEA2700:01C561A4] X-Spam-Status: No, score=1.8 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST,MSGID_FROM_MTA_HEADER autolearn=no version=3.0.3 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hi! everyone, I am looking for reference study results on the energy and structure data on O2 and O atom, both experimental and theoretical to compare with my calculation results. Can you give me a hand? Sincerely yours Xin, Liu _________________________________________________________________ FREE pop-up blocking with the new MSN Toolbar get it now! http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/ From chemistry-request@ccl.net Thu May 26 02:17:53 2005 Received: from web41904.mail.yahoo.com (web41904.mail.yahoo.com [66.218.93.155]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j4Q6Hm3A027443 for ; Thu, 26 May 2005 02:17:49 -0400 Received: (qmail 63493 invoked by uid 60001); 26 May 2005 06:17:48 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=dBsVGY9GUkcLFpS2swsBvV2RYThRBIK2S2CIflvJ7f3WFrfSAxdnC3vWdDRT+fL99VVb1687SuFcM0x7rg6iH+uGQY7E3FpmYoUawWmz5FujSgidCaP0KEaKmo9DWDRUcNRomGpQLGXYN6Rbh1HDbeKEy9N8sWBmudWIuLf20pA= ; Message-ID: <20050526061747.63491.qmail = = = web41904.mail.yahoo.com> Received: from [128.139.226.37] by web41904.mail.yahoo.com via HTTP; Wed, 25 May 2005 23:17:47 PDT Date: Wed, 25 May 2005 23:17:47 -0700 (PDT) From: limor harel Subject: ozone To: ccl MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1290648024-1117088267=:62723" X-Spam-Status: No, score=1.8 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST,HTML_50_60,HTML_MESSAGE autolearn=no version=3.0.3 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net --0-1290648024-1117088267=:62723 Content-Type: text/plain; charset=us-ascii Hi all, I would like to get an information about kinetics and dinamics in ozone layer. Thanks, Limor --------------------------------- Do You Yahoo!? Yahoo! Small Business - Try our new Resources site! --0-1290648024-1117088267=:62723 Content-Type: text/html; charset=us-ascii
Hi all,
I would like to get an information about kinetics and dinamics in ozone layer.
 
Thanks,
 
Limor

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Yahoo! Small Business - Try our new Resources site! --0-1290648024-1117088267=:62723-- From chemistry-request@ccl.net Thu May 26 11:40:47 2005 Received: from idmailgate2.unizh.ch (idmailgate2.unizh.ch [130.60.68.106]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4QFefOl016203 for ; Thu, 26 May 2005 11:40:41 -0400 Received: from zimail1.unizh.ch (zimail1.unizh.ch [130.60.128.11]) by idmailgate2.unizh.ch (8.13.1/8.13.1/SuSE Linux 0.7) with ESMTP id j4QEc2BS007142 for ; Thu, 26 May 2005 16:38:08 +0200 Received: from zisgi.unizh.ch (zisgi.unizh.ch [130.60.68.15]) by zimail1.unizh.ch (8.12.10/8.12.10/smMTA-17) with ESMTP id j4QEbv2Q005985 for ; Thu, 26 May 2005 16:38:02 +0200 (MEST) Date: Thu, 26 May 2005 16:37:57 +0200 From: "Dr. Peter Burger" To: CHEMISTRY !=! ccl.net Subject: CCL:g03 & Intel Fortran (32 bit) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by amavisd-new X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear CCLers, anyone willing to share details on how to compile (modify) gaussian 03 rev C02 with the 32 bit Intel Fortran compiler (rev 8.1)? Many thanks in advance Peter From chemistry-request@ccl.net Thu May 26 12:54:21 2005 Received: from tiziano.phys.washington.edu (tiziano.phys.washington.edu [128.95.93.135]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4QGsIFH020177 for ; Thu, 26 May 2005 12:54:19 -0400 Received: from tiziano.phys.washington.edu (localhost.localdomain [127.0.0.1]) by tiziano.phys.washington.edu (8.12.11/8.12.11) with ESMTP id j4QGpM9w011078 for ; Thu, 26 May 2005 09:51:22 -0700 Received: from localhost (fer@localhost) by tiziano.phys.washington.edu (8.12.11/8.12.11/Submit) with ESMTP id j4QGpLmX011074 for ; Thu, 26 May 2005 09:51:22 -0700 Date: Thu, 26 May 2005 09:51:21 -0700 (PDT) From: "Fernando D. Vila" To: Computational Chemistry List Subject: Compact gamma-alumina (110) cell Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hello everybody. I'm trying to do some simulations of the interaction of Re on athe (110) surface of gamma-Al2O3. The problem I have is that g-Al2O3 seems to be a pretty nasty system (At least for a surface simulations begginer like me :-). I have a paper by Wolverton where they declare that after checking the different options they have, they found a nice compact (i.e. similar axis lengths) and small cell to do the simulations on bulk alumina. I have been trying to create this cell for some time now without success. What I'm wondering is if anybody here has some expertise with g-Al2O3, can maybe tell me how to build that cell. Maybe also send me some examples of cells that I could use to guide me. Any help would be very greatly appreciated. Best regards and thanks in advance, Fer. Ubi dubium ibi libertas. ******************************************************************************* Fernando D. Vila Voice (206)543-9697 Department of Physics Fax (206)685-0635 University of Washington E-mail fdv-.at.-u.washington.edu Seattle, WA 98195, USA WWW http://faculty.washington.edu/fdv *******************************************************************************