From chemistry-request@server.ccl.net Mon Oct 14 04:50:27 2002 Received: from netra.ksu.edu.sa ([212.138.39.67]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9E8oNf20812 for ; Mon, 14 Oct 2002 04:50:24 -0400 Received: from sun1.ksu.edu.sa (sun1.ksu.edu.sa [212.138.39.3]) by netra.ksu.edu.sa (8.9.0/8.9.0) with ESMTP id MAA02448 for ; Mon, 14 Oct 2002 12:15:11 -1700 (Mideast/Riyadh) Received: from localhost (azhary@localhost) by sun1.ksu.edu.sa (8.9.0/8.7.3) with SMTP id LAA19029 for ; Mon, 14 Oct 2002 11:43:09 -0300 (GMT) Date: Mon, 14 Oct 2002 11:43:08 -0300 (GMT) From: "Adel Abbas Ali Elazhary Sci. College" X-Sender: azhary@sun1 To: chemistry@ccl.net Subject: Alchemy 2000 MM3 energy Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL netters: I am doing a conformational search using the alchemy 2000 program and I do MM3 geometry optimization of each predicted conformation. I found that the MM3 energy value of the optimized conformations is not consistent. I mean after doing MM3 geometry optimzation energy of say 10 conformations and recalculating them again it is not ncessary to get the same MM3 energy value. Since my molecule has a ring of about 20 atoms I did the calculations for a similar smaller ring system and I found that the energy values are consistent which means that the problem is with my molecule only. I printed the output file with different MM3 energy values for the same conformation and I noticed that there is a difference of 0.00001 A in the coordinates of some atoms and a difference of 0.0002 in the initial steric energy values and after the geometry optimization each output has a different route with quite different final energy and geometry. I would greatly appreciate it if some one noticed this before and know a solution to this problem to inform me. Thank you very much in advance. Best regards, Adel El-azhary From chemistry-request@server.ccl.net Mon Oct 14 08:57:36 2002 Received: from albireo.uni-muenster.de ([128.176.214.183]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9ECvaf25276 for ; Mon, 14 Oct 2002 08:57:36 -0400 Received: by albireo.uni-muenster.de (Postfix on SuSE Linux 7.3 (i386), from userid 500) id 115EE1F978; Mon, 14 Oct 2002 10:45:59 +0200 (CEST) Content-Type: text/plain; charset="iso-8859-15" From: Stefan Grimme Reply-To: grimmes@uni-muenster.de Organization: Universitaet Muenster To: chemistry@ccl.net Subject: CCL: modelling for biologists Date: Mon, 14 Oct 2002 10:45:58 +0200 X-Mailer: KMail [version 1.3.2] MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Message-Id: <20021014084559.115EE1F978@albireo.uni-muenster.de> Dear all, we want to give a two day course on molecular modelling to undergraduate biologists, just an introduction to show what in principal can be done with e.g. simple force-fields. Has anybody ideas/worked-out examples for that purpose? (should be simple and practicable with a MM program equipped with a graphical interface). Thanks a lot. Best regards, Stefan _________________________________________________________ Prof. Dr. Stefan Grimme Organisch-Chemisches Institut (Abt. Theoretische Chemie) Westfaelische Wilhelms-Universitaet, Corrensstrasse 40 D-48149 Muenster, Tel (+49)-251-83 36512/33241/36515(Fax) Email:grimmes@uni-muenster.de http://www.uni-muenster.de/Chemie/OC/research/grimme/ _________________________________________________________ Positions available for carrying out doctoral or postdoctoral studies in chemistry in Münster: http://www.uni-muenster.de/Chemie/OC/positions/ _________________________________________________________ From chemistry-request@server.ccl.net Mon Oct 14 04:30:07 2002 Received: from mailstudenti.unimi.it ([159.149.10.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9E8U7f20400 for ; Mon, 14 Oct 2002 04:30:07 -0400 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailstudenti.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0H3Y00JL3PZ0BN@mailstudenti.unimi.it> for chemistry@ccl.net; Mon, 14 Oct 2002 10:23:25 +0200 (MEST) Received: from Villa (villa.farma.unimi.it [159.149.79.66]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with SMTP id <0H3Y00IH7PY3CD@smtp.unimi.it> for chemistry@ccl.net; Mon, 14 Oct 2002 10:23:26 +0200 (MEST) Date: Mon, 14 Oct 2002 10:22:40 +0200 From: Giulio Vistoli Subject: Re: CCL:software to plot ligand-protein interaction To: amor san juan , chemistry@ccl.net Message-id: <004b01c2735a$dcb0f270$424f959f@Villa> Organization: =?iso-8859-1?Q?Universit=E0_di_Milano?= MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-Mailer: Microsoft Outlook Express 6.00.2800.1106 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal References: <20021013100813.70910.qmail@web12804.mail.yahoo.com> Dear Amor, VEGA (http://www.ddl.unimi.it) is able to calculate and visualize the intermolecular interactions in a ligand+protein complex. It is very useful in the complex analysis as it calculates and shows only the residues that are involved in complex stabilization (i.e. with a residue energy grater than a user defined percentage) Best regards Giulio From chemistry-request@server.ccl.net Mon Oct 14 02:32:46 2002 Received: from web13205.mail.yahoo.com ([216.136.174.190]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g9E6Wjf18371 for ; Mon, 14 Oct 2002 02:32:45 -0400 Message-ID: <20021014063241.48387.qmail@web13205.mail.yahoo.com> Received: from [195.87.181.87] by web13205.mail.yahoo.com via HTTP; Sun, 13 Oct 2002 23:32:41 PDT Date: Sun, 13 Oct 2002 23:32:41 -0700 (PDT) From: Dennis Ryan Subject: Monte Carlo software To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1240477826-1034577161=:48231" --0-1240477826-1034577161=:48231 Content-Type: text/plain; charset=us-ascii Hello, Are there any suggestions of Monte Carlo software that can be used for specific determination of hydrogen bonds in a solvent? Thanks in advance Best Regards Dennis --------------------------------- Do you Yahoo!? Faith Hill - Exclusive Performances, Videos, & more faith.yahoo.com --0-1240477826-1034577161=:48231 Content-Type: text/html; charset=us-ascii

Hello,

Are there any suggestions of Monte Carlo software that can be used for specific determination of hydrogen bonds in a solvent?

Thanks in advance

Best Regards

Dennis


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faith.yahoo.com --0-1240477826-1034577161=:48231-- From chemistry-request@server.ccl.net Mon Oct 14 09:28:35 2002 Received: from mum.mans.edu.eg ([193.227.50.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9EDSXf25924 for ; Mon, 14 Oct 2002 09:28:35 -0400 Received: by mum.mans.edu.eg with Internet Mail Service (5.5.2656.59) id <47MK4HXF>; Mon, 14 Oct 2002 15:30:51 +0200 Message-ID: <4C7A402190F4BD4385075D6B739AB4141394F7@mum.mans.edu.eg> From: Tarek Mamoun El-Gogary To: "'CHEMISTRY@ccl.net'" Subject: computed and observed band positions Date: Mon, 14 Oct 2002 15:30:50 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2656.59) Content-Type: text/plain Dear CCLERs, I am doing a CI calculation on some oganic molecules to compute the UV-VIS sepctrum. I found that: 1- poor agreement between computed and observed band positions 2- the AM1 band positions are closer to the observed ones than that calculated using ab-initio method. I am using G98. Could anyone comment on these findings. thanks sin advance Tarek From chemistry-request@server.ccl.net Mon Oct 14 12:00:52 2002 Received: from internal.cambridgesoft.com ([198.112.109.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9EG0qf30138 for ; Mon, 14 Oct 2002 12:00:52 -0400 Received: from [172.16.1.122] ([172.16.1.122]) by internal.cambridgesoft.com with Microsoft SMTPSVC(5.0.2195.4905); Mon, 14 Oct 2002 12:00:52 -0400 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Sender: jsb@exchange.cambridgesoft.com Message-Id: In-Reply-To: Date: Mon, 14 Oct 2002 12:00:54 -0400 To: Maneesh Yadav From: Jonathan Brecher Subject: Re: CCL:IChi ref? Cc: chemistry@ccl.net X-OriginalArrivalTime: 14 Oct 2002 16:00:52.0575 (UTC) FILETIME=[DF25CEF0:01C2739A] At 9:11 PM -0400 10/12/02, Maneesh Yadav wrote: >With respect to the new chemical nomenclature system being propsed by >IUPAC, can anyone confirm or deny the existence of a published paper >descibring the system? > >I realize it's still a work in progress, but I would like to talk about >chemical nomenclature in an upcoming journal club, and it'd be hard to >talk about IChi if I couldn't find a ref. If anyone could point me to >some sources which describe the nomenclature system in a little more >detail than in the Nature and Alchemist clippings I'd be grateful. Go to http://www.iupac.org Type "ichi" in the search box The first link is http://www.iupac.org/projects/2000/2000-025-1-800.html It's a stretch to say that the IChI project has much of anything to do with nomenclature. Jonathan Brecher CambridgeSoft Corporation jsb@cambridgesoft.com