From chemistry-request@ccl.net Tue Apr 19 22:00:47 2005 Received: from web30102.mail.mud.yahoo.com (web30102.mail.mud.yahoo.com [68.142.200.75]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j3K20ghX010152 for ; Tue, 19 Apr 2005 22:00:43 -0400 Received: (qmail 58060 invoked by uid 60001); 20 Apr 2005 01:00:37 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=Sio2wWmd0tLNJhBPqYItlKgbBUCDnwZWTwbZ5MXhy/PuaXyr1d4YDU851kXvdBBr77ugAPXa5SHHZ1+7NpncZV7cL62N9NOyUslljFaoRURAD7Y9BVLiNUu9tIsUw+EZZUkiC1QxRvZh6suhCHMKk+z2UE9tIPseR1ysHqSKMF0= ; Message-ID: <20050420010037.58058.qmail * web30102.mail.mud.yahoo.com> Received: from [202.127.145.15] by web30102.mail.mud.yahoo.com via HTTP; Tue, 19 Apr 2005 18:00:37 PDT Date: Tue, 19 Apr 2005 18:00:37 -0700 (PDT) From: Jinming zhou Subject: develop miss parameters of opls force field To: ccl MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-755655211-1113958837=:57592" X-Spam-Status: No, score=2.6 required=5.0 tests=DNS_FROM_RFC_ABUSE, FORGED_YAHOO_RCVD,HTML_30_40,HTML_MESSAGE autolearn=no version=3.0.1 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net --0-755655211-1113958837=:57592 Content-Type: text/plain; charset=us-ascii dear ccler i want to to develop opls ff parameter of an unusial molecule, in principle, such parameter can be derived from QM calculation. but i don't exactly know it, can some body give some advice or list some papers about that. thank you very much! Jinming --------------------------------- Do you Yahoo!? Yahoo! Small Business - Try our new resources site! --0-755655211-1113958837=:57592 Content-Type: text/html; charset=us-ascii
dear ccler
 
i want to to develop opls ff parameter of an unusial molecule, in principle, such parameter can be derived from QM calculation.  but i don't exactly know it, can some body give some advice or list some papers about that. thank you very much!

Jinming


Do you Yahoo!?
Yahoo! Small Business - Try our new resources site! --0-755655211-1113958837=:57592-- From chemistry-request@ccl.net Wed Apr 20 02:22:08 2005 Received: from web41109.mail.yahoo.com (web41109.mail.yahoo.com [66.218.93.25]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j3K6M3JM024638 for ; Wed, 20 Apr 2005 02:22:04 -0400 Received: (qmail 59821 invoked by uid 60001); 20 Apr 2005 05:22:02 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=wtMp7CqDUG5wu1bkQr+E4WA7sFzp73A8rK9CQMKNz402zAip+1VIc9j60mdUm0V37olTY8wjbGSnOEbskhkPAZODShuHHUIABkZGKnFKGu9/1i1o6ymWGHL0zt+pPKyTo6m/yfIVCkGPNNgcwoRI7gSpSI5+XLmvzVJgTpErnTk= ; Message-ID: <20050420052202.59819.qmail :: web41109.mail.yahoo.com> Received: from [217.218.86.55] by web41109.mail.yahoo.com via HTTP; Wed, 20 Apr 2005 06:22:02 BST Date: Wed, 20 Apr 2005 06:22:02 +0100 (BST) From: anita abedi Subject: NMR To: chemistry :: ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-320045401-1113974522=:59031" Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE, HTML_MESSAGE autolearn=no version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net --0-320045401-1113974522=:59031 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit GOOD DAY I am a scholar in Azad university in Iran. I study on 2J coupling constant in NMR, and I wanted the experimental data is compaired with calculation results, so I need deMon NMR program. I need informations about buying this program and how using of it. I'm waiting your answer. thank you very much again. Anita Abedi TEL : 98 21 2083747 FAX : 98 21 2083747 --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now --0-320045401-1113974522=:59031 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit

GOOD DAY

I am a scholar in  Azad university in Iran. I study on 2J coupling constant in NMR, and I wanted the experimental data is compaired with calculation results, so I need deMon NMR program.

I need informations about buying this program and how using of it.

I'm waiting your answer.

thank you very much again.

Anita Abedi

 

TEL :  98 21 2083747

FAX :  98 21 2083747

 

Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now --0-320045401-1113974522=:59031-- From chemistry-request@ccl.net Wed Apr 20 13:19:43 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3KHJgPu010329 for ; Wed, 20 Apr 2005 13:19:42 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j3KHJg7W010328 for chemistry :: ccl.net; Wed, 20 Apr 2005 13:19:42 -0400 Date: Wed, 20 Apr 2005 13:19:42 -0400 Message-Id: <200504201719.j3KHJg7W010328 :: server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request :: ccl.net using -f From: "serdar, , durdagi" To: chemistry :: ccl.net X-Web-Message-Number: 050420131754-10194 Subject: W:castep X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Hi, I am using CASTEP program at my calculations..When I submitting a job, at quing system it seems running, but when I looked to scratch file there is no line in output file and nothing also in error file..Could anybody tell me what is problem there? thanks for any assistance.. Serdar Durdagi From chemistry-request@ccl.net Tue Apr 19 22:25:08 2005 Received: from nmd.dbtd.dca.wayport.net ([207.250.179.82]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3K2P2ME012436 for ; Tue, 19 Apr 2005 22:25:03 -0400 Received: from nmd.dbtd.dca.wayport.net (localhost [[UNIX: localhost]]) by nmd.dbtd.dca.wayport.net (8.12.10/8.12.10) with ESMTP id j3K16Dw2008549 for ; Tue, 19 Apr 2005 21:06:13 -0400 Message-ID: <001701c54545$2667bd40$471fc242 :: at.amphoracorp.com> From: "Jennifer Miller" To: Subject: Call for Papers: Special Issue on Applications of Geometric Modeling in the Life Sciences. Date: Tue, 19 Apr 2005 21:06:13 -0400 MIME-Version: 1.0 Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2900.2180 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-Spam-Status: No, score=0.5 required=5.0 tests=DNS_FROM_RFC_WHOIS autolearn=no version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Computer Aided Geometric Design http://authors.elsevier.com/journal/cagd Call for Papers Special Issue on Applications of Geometric Modeling in the Life Sciences. Guest Editors: Hans J. Wolters (Celera Genomics) and Bernd Hamann (UC Davis) CAGD is the premier journal for publications related to geometric design and modeling. Geometric Modeling comprises all methods that are based on concepts from applied geometry as well as computational geometry with emphasis on methods that use three-dimensional techniques. In order to expand the application domains of geometric modeling, CAGD is seeking original papers for a special issue on Applications of Geometric Modeling in the Life Sciences. The goal is to bridge the gap between geometric modeling and applications in the life sciences. For example, we are interested in novel geometric modeling approaches in areas like brain modeling, computational biology, and computational chemistry. Further, three-dimensional modeling techniques as applied to developing new descriptors and representations for macromolecules (proteins) as well as small molecules are of interest. Papers may also address computational drug discovery, where shape is a major consideration together with chemical features. In summary, the papers submitted should address novel geometric modeling approaches in the following, or closely related, areas: - Computational drug discovery - Protein structure modeling and folding - Molecular surfaces and its descriptors - Modeling of brain structure and other organs - Computational and mathematical biology and bioinformatics Important Dates: Submission Deadline: July 1st, 2005 Notification: August 15th, 2005 Revised Manuscript Submission: September 15th, 2005 Revised Manuscript Notification: October 15th, 2005 Final Version Due: November 1st, 2005 Electronic Submission: Papers should be submitted electronically via the new submission system of Computer-Aided Geometric Design, which will be available around May 15th at http://ees.elsevier.com/cagd/. This page is currently still under construction. Please do not submit your paper as long as this site is still under construction. Detailed formatting instructions are available at http://authors.elsevier.com/journal/cagd. All submissions will be reviewed in accordance with the usual standards of CAGD, hence all dates but the submission deadline are tentative. Hans J. Wolters Bernd Hamann Celera Genomics Department of Computer Science 180 Kimball Way University of California, Davis South San Francisco, CA 94080 One Shields Avenue USA USA hans.wolters :: celera.com hamann :: cs.ucdavis.edu From chemistry-request@ccl.net Tue Apr 19 22:48:31 2005 Received: from simbiosys.ca ([65.18.214.160]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3K2mRuL014456 for ; Tue, 19 Apr 2005 22:48:27 -0400 Received: from phobos.simbiosys.ca (CPE00036df36d8d-CM000f9f809310.cpe.net.cable.rogers.com [69.193.210.79]) (authenticated) by simbiosys.ca (8.11.6/8.11.6) with ESMTP id j3K0VO727960 for ; Tue, 19 Apr 2005 20:31:28 -0400 From: Aniko Simon Organization: SimBioSys Inc. To: CCL Subject: CCL: announcing eHiTS: free docking software for teaching and academic research Date: Tue, 19 Apr 2005 21:28:10 -0400 User-Agent: KMail/1.5.3 MIME-Version: 1.0 Content-Disposition: inline Message-Id: <200504192124.18236.aniko * simbiosys.ca> Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net SimBioSys offers eHiTS 5.1 free for teaching and academic research! eHiTS is the truly exhaustive docking program that explores the full conformational and pose space. The newly released version 5.1 ships with a fully automated training facility that can tune the scoring function to particular receptors or protein families, improving both accuracy and enrichment results. eHiTS consistently outperforms other docking tools in validation comparisons, using publically available datasets, resulting in more accurate docking poses. In addition, the automated handling of protontation states produces more accurate screening results for large databases, where up-front estimating of the protonation states for all ligand/receptor combinations is impossible. eHiTS evaluates all possible protonation states in a single run. To further improve the great results of eHiTS, the new training facility allows the user to tailor the scoring functions to recognize particular families of interest and better score ligands that make key interactions. The training utility is very simple to use and can improve both accuracy and enrichment results. SimBioSys recognizes the importance of docking research in the academic world, and the financial constraints of many academic institutions. With this in mind, we are offering eHiTS 5.1 free for most academic institutions. For more information about eHiTS 5.1 and to obtain an evaluation of the software, please visit our website (www.simbiosys.ca) and fill out a demo request form. From chemistry-request@ccl.net Wed Apr 20 08:41:38 2005 Received: from sender-01.it.helsinki.fi (sender-01.it.helsinki.fi [128.214.205.139]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3KCfWPA017032 for ; Wed, 20 Apr 2005 08:41:33 -0400 Received: from soul.it.helsinki.fi (soul.it.helsinki.fi [128.214.189.108]) by sender-01.it.helsinki.fi (8.13.3/8.13.3) with ESMTP id j3KBRPPl031360; Wed, 20 Apr 2005 14:27:25 +0300 Received: from soul.it.helsinki.fi (localhost [127.0.0.1]) by soul.it.helsinki.fi (8.12.10/8.12.10) with ESMTP id j3KBROIg032163; Wed, 20 Apr 2005 14:27:24 +0300 (EEST) Received: from localhost (mpjohans@localhost) by soul.it.helsinki.fi (8.12.10/8.12.10/Submit) with ESMTP id j3KBRO57032160; Wed, 20 Apr 2005 14:27:24 +0300 (EEST) X-Authentication-Warning: soul.it.helsinki.fi: mpjohans owned process doing -bs Date: Wed, 20 Apr 2005 14:27:24 +0300 (EEST) From: Mikael Johansson X-X-Sender: mpjohans -()- soul.it.helsinki.fi To: "Noel O'Boyle" cc: chemistry -()- ccl.net Subject: Re: CCL:Effect of oxidation on electron density In-Reply-To: <1113920796.31132.16.camel -()- drugs.ucd.ie> Message-ID: References: <1113920796.31132.16.camel -()- drugs.ucd.ie> MIME-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="1824380544-245302103-1113996444=:32070" X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. --1824380544-245302103-1113996444=:32070 Content-Type: TEXT/PLAIN; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: QUOTED-PRINTABLE Hello Noel and All! On Tue, 19 Apr 2005, Noel O'Boyle wrote: > I am using Gaussian03 and have calculated the electron density of the > molecule in its oxidised state (at the geometry of the native state) and > subtracted this from the electron density of the molecule in its native > state. > > However, I have just noticed that the total spin density of the oxidised > molecule gives an almost identical picture. Is this true in general? (I > don't have a good understanding of what the total spin density shows.) No. Spin density and total electron density difference are two different=20 and more or less independent creatures, though they _can_ be located to=20 similar regions of the molecule (as apparently for you). Spin density is=20 much more free to change after, for example, oxidation/reduction. The=20 electron density is much more restricted as it is bound by classical=20 electrostatic forces. I've done some studies comparing electron and spin density changes during= =20 oxidation/reduction of iron porphyrins [1-3]. Perhaps they are of some=20 interest. Have a nice day, Mikael J. http://www.helsinki.fi/~mpjohans/ [1] M.P. Johansson, M.R.A. Blomberg, D. Sundholm, M. Wikstr=F6m, "Change in electron and spin density upon electron transfer to haem", Biochim. Biophys. Acta - Bioenergetics 1553 (2002) 183-187. [2] M.P. Johansson, D. Sundholm, G. Gerfen, M. Wikstr=F6m, "The Spin Distribution in Low-Spin Iron Porphyrins", J. Am. Chem. Soc. 124 (2002) 11771-11780 [3] M.P. Johansson, D. Sundholm, "Spin and charge distribution in iron porphyrin models: A coupled cluster and density-functional study", J. Chem. Phys. 120 (2004) 3229-3236. --1824380544-245302103-1113996444=:32070--