From chemistry-request@ccl.net Tue Nov 23 05:59:41 2004 Received: from sainfoin.extra.cea.fr (sainfoin.extra.cea.fr [132.166.172.103]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iANAxd1u002270 for ; Tue, 23 Nov 2004 05:59:40 -0500 Received: from araneus.saclay.cea.fr (araneus.saclay.cea.fr [132.166.192.110]) by sainfoin.extra.cea.fr (8.12.10/8.12.10/CEAnet-Internet.4.0) with ESMTP id iANBDrbV022803 for ; Tue, 23 Nov 2004 12:13:53 +0100 (MET) Received: from nenuphar.saclay.cea.fr (unverified) by araneus.saclay.cea.fr (Content Technologies SMTPRS 4.3.17) with ESMTP id for ; Tue, 23 Nov 2004 12:13:53 +0100 Received: from llb.saclay.cea.fr (llb.saclay.cea.fr [132.166.17.100]) by nenuphar.saclay.cea.fr (8.12.10/8.12.10/CEAnet-internes.4.0) with ESMTP id iANBDrgi008479 for ; Tue, 23 Nov 2004 12:13:53 +0100 (MET) Received: from [132.166.18.220] (llb1220.saclay.cea.fr [132.166.18.220]) by llb.saclay.cea.fr (8.12.10/jtpda-5.3.2) with ESMTP id iANBDpeC026507 for ; Tue, 23 Nov 2004 12:13:52 +0100 (MET) Mime-Version: 1.0 (Apple Message framework v619) Message-Id: Content-Type: text/plain; charset=ISO-8859-1; format=flowed To: CCL computational chemistry list (E-mail) From: hinsen)at(llb.saclay.cea.fr Subject: New search engine for the academic world Date: Tue, 23 Nov 2004 12:15:17 +0100 X-Mailer: Apple Mail (2.619) X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id iANAxf1u002278 Google has a new search engine (in beta testing) for academic papers and related documents. Have a look at http://www.scholar.google.com/ for all the details. -- --------------------------------------------------------------------- Konrad Hinsen Laboratoire Lion Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: hinsen)at(llb.saclay.cea.fr --------------------------------------------------------------------- From chemistry-request@ccl.net Tue Nov 23 09:06:17 2004 Received: from gveu50.emea.givaudan.com (mail-external3.givaudan.com [57.66.141.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iANE6F1u020354; Tue, 23 Nov 2004 09:06:16 -0500 To: "Computational Chemistry List" Cc: chemistry)at(ccl.net Subject: Software for Material Science MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: andras.borosy)at(givaudan.com Date: Tue, 23 Nov 2004 15:20:29 +0100 X-MIMETrack: Serialize by Router on gvedoh01/H/Givaudan(Release 5.0.12 |February 13, 2003) at 23/11/2004 15:20:36, Serialize complete at 23/11/2004 15:20:36 Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=2.0 required=7.5 tests=IMPRONONCABLE_1,NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id iANE6H1u020358 Dear Colleagues, Several months ago I asked you about the alternatives to Accelrys' Material Studio. They can be as follows: At microscopic level: Materials and Processes Simulations (MAPS) platform of Scienomics (www.scienomics.com). At mesoscopic level: AlCove (www.molecular-dynamics.de). Best regards, Dr. Andras Borosy Seniour Scientist Delivery Systems, Fragrance Research Givaudan Schweiz AG Ueberlandstr. 138 8600 D|bendorf Switzerland tel: + 41-1-8242164 fax: +41-1-8242926 e-mail: andras.borosy)at(givaudan.com From chemistry-request@ccl.net Tue Nov 23 08:53:08 2004 Received: from ppsw-2.csi.cam.ac.uk (ppsw-2.csi.cam.ac.uk [131.111.8.132]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iANDr51u019193 for ; Tue, 23 Nov 2004 08:53:06 -0500 Received: from hermes-1.csi.cam.ac.uk ([131.111.8.51]:54062) by ppsw-2.csi.cam.ac.uk (ppsw.cam.ac.uk [131.111.8.132]:25) with esmtp id 1CWbK7-000865-98 (Exim 4.43) for chemistry..at..ccl.net (return-path ); Tue, 23 Nov 2004 14:07:15 +0000 Received: from prayer by hermes-1.csi.cam.ac.uk with local (Exim 4.34) id 1CWbK2-0003R6-5o for chemistry..at..ccl.net; Tue, 23 Nov 2004 14:07:10 +0000 From: Andreas Bender To: chemistry..at..ccl.net Subject: "New Horizons in Molecular Informatics", Cambridge/UK, 7/12/2004 Date: 23 Nov 2004 14:07:10 +0000 X-Mailer: Prayer v1.0.11 X-Originating-IP: [131.111.121.25] Message-ID: Mime-Version: 1.0 Content-Type: text/plain; format=flowed; charset=ISO-8859-1 X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned X-Spam-Status: No, hits=3.0 required=7.5 tests=FROM_ENDS_IN_NUMS, MAILTO_TO_SPAM_ADDR autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL'lers, I would like to invite you to a one-day symposium taking place in Cambridge/UK on 7 December 2004 on "New Horizons to Molecular Informatics" The (slightly abstract) text from the conference brochure: "This symposium addresses how we can best create, manipulate and integrate molecular data to deepen our understanding of molecules and their properties and to allow novel in-silico experimentation. In particular, speakers will discuss optimising the chances of discovery resulting from applications of informatics technologies." To give a few keywords: in-silico metabolic pathways, virtual screening, bioinformatics and society, computer-aided drug discovery to improve attrition rates, representation of chemical information (CML/XML) and applications of electronic notebooks will be discussed. Speakers include Johann Gasteiger (University of Erlangen, Germany), Peter Willett (University of Sheffield, England), Michael Ashburner (European Bioinformatics Institute, Cambridge, England), Jonathan Mason (Pfizer Global Research & Development), Peter Murray-Rust (University of Cambridge, England) and Allan Ferguson (Merck & Co.). More information can be found at http://www.mmsconferencing.com/informatics.html and the complete program can be downloaded from http://www.mmsconferencing.com/pdf/New_Horizons_Brochure_final.pdf For those interested and staying overnight I can also offer a guided tour through the historical pubs of Cambridge after the symposium. Best wishes, Andreas -- ab454..at..cam.ac.uk - Andreas.Bender..at..Alumni.TU-Berlin.DE Andreas Kieron Patrick Bender http://www.andreasbender.de From chemistry-request@ccl.net Tue Nov 23 14:17:31 2004 Received: from maya.uab.es (maya.uab.es [158.109.0.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iANJHT37014339 for ; Tue, 23 Nov 2004 14:17:30 -0500 Received: from CONVERSION-DAEMON.maya.uab.es by maya.uab.es (PMDF V6.2-X20 #30859) id <0I7N00B01CVXST(at)maya.uab.es> for chemistry(at)ccl.net; Tue, 23 Nov 2004 20:31:13 +0100 (MET) Received: from gavatx.qf.uab.es (gavatx.qf.uab.es [158.109.14.75]) by maya.uab.es (PMDF V6.2-X20 #30859) with SMTP id <0I7N00M2VCVWMB(at)maya.uab.es>; Tue, 23 Nov 2004 20:31:08 +0100 (MET) Received: by gavatx.qf.uab.es (sSMTP sendmail emulation); Tue, 23 Nov 2004 20:35:22 +0100 Date: Tue, 23 Nov 2004 20:35:22 +0100 From: Oriol Vendrell Subject: Re: CCL:CIS opt on G03 problem In-reply-to: <419E38DD.14386.FB0D524(at)mail.dct.tudelft.nl> To: Martijn Zwijnenburg Cc: chemistry(at)ccl.net Message-id: <20041123193522.GA14568(at)gavatx.qf.uab.es> Dear Martijn, I found the same problem with g98 two or three years ago. After looking unfruitfully for information on what Tx T could be and trying to fi= nd and IOP that would suppress such an annoyng behaviour I took the quick and dirty way: I looked for the line of code inside the link 1014 which performs the test and decides wether to terminate or not, I commented it out and recompiled the link. It is fine to do it since you'll go to the optimized structure, and close to the stationary point such a problem is not encountered again, meaning that your results are fine. Hope it helps, Oriol Oriol Vendrell Romagosa e-mail: oriol(at)qf.uab.es Unitat de Qu=EDmica F=EDsica phone: +34 93 581 28 14 Departament de Qu=EDmica fax: +34 93 581 29 20 Universitat Aut=F2noma de Barcelona www: http://www.qf.uab.es/oriol 08193 Bellaterra, Catalunya Spain From chemistry-request@ccl.net Tue Nov 23 15:24:29 2004 Received: from neptune.tranzyme.com (neptune.tranzyme.com [132.210.158.201]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iANKOSSj020375 for ; Tue, 23 Nov 2004 15:24:29 -0500 Received: from mercure.tranzyme.com (dcsher01.tranzyme.com [192.168.1.3]) by neptune.tranzyme.com (8.12.10/8.12.10) with ESMTP id iANKcaIr002774 for ; Tue, 23 Nov 2004 15:38:48 -0500 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C4D19C.7C51E824" X-MimeOLE: Produced By Microsoft Exchange V6.5.7226.0 Subject: CCL: ForceFields for macrocycles Date: Tue, 23 Nov 2004 15:39:09 -0500 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: CCL: ForceFields for macrocycles Thread-Index: AcTRnHviEHF2ix5SRoyr8QIdHIFGww== From: "Axel Mathieu" To: "CCL" X-Scanned-By: MIMEDefang 2.48 on 192.168.1.1 X-Spam-Status: No, hits=0.1 required=7.5 tests=HTML_70_80,HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------_=_NextPart_001_01C4D19C.7C51E824 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Greetings to all, =20 I've been having a discussion with some of my colleagues about = forcefields and the question came about the use of a proper forcefields = for macrocyclic molecules, given our recent NMR developments here. I've = been modeling these types of molecules for about 2 years now and have = been using a modified MMFFF94s forcefield for all conformational = searches for various reasons but mostly as this in my opinion, is the = best forcefield at hand for me right now. =20 Are any of you aware of special forcefields or have developed a specific = forcefield for macrocycles? Or then again, what forcefields are you = using for macrocyles? Your opinion/experience on this is most valuable = to me. =20 Again, many thanks to the CCL community for your never ending help, =20 APM =20 ------_=_NextPart_001_01C4D19C.7C51E824 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Greetings to all,

 

I’ve been having a discussion with some of my colleagues about forcefields and the = question came about the use of a proper forcefields for = macrocyclic molecules, given our recent NMR = developments here. I’ve been modeling these types of molecules for about 2 years now = and have been using a modified MMFFF94s forcefield for all conformational searches for various reasons but mostly as this in my opinion, is the best forcefield at hand for = me right now.

 

Are any of you aware of special forcefields or have developed a specific forcefield for = macrocycles? Or then again, what forcefields are you using for macrocyles? Your = opinion/experience on this is most valuable to me.

 

Again, many thanks to the = CCL community for your never ending = help,

 

APM

 

------_=_NextPart_001_01C4D19C.7C51E824-- From chemistry-request@ccl.net Tue Nov 23 15:18:49 2004 Received: from mx.seanet.com (mx.seanet.com [199.181.164.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iANKIlSj019906 for ; Tue, 23 Nov 2004 15:18:48 -0500 Received: from pepeketua.seanet.com (pepeketua.seanet.com [199.181.164.73]) by milkyway.seanet.com (8.13.1/8.13.1) with ESMTP id iANKWpxq027731 for ; Tue, 23 Nov 2004 12:32:51 -0800 (PST) (envelope-from mark-.at.-arguslab.com) Received: from planaria (c-24-18-182-93.client.comcast.net [24.18.182.93]) by pepeketua.seanet.com (Postfix) with ESMTP id 3B0F111473 for ; Tue, 23 Nov 2004 12:33:07 -0800 (PST) Reply-To: From: "Mark Thompson" To: Subject: RE: Solvate in ArgusLab Date: Tue, 23 Nov 2004 12:33:05 -0800 Message-ID: <000401c4d19b$a29fe360$0300a8c0@planaria> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.6604 (9.0.2911.0) X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 Importance: Normal In-Reply-To: <3khj1f$crvogm-.at.-mxip06a.cluster1.charter.net> X-Spam-Status: No, hits=2.6 required=7.5 tests=RCVD_IN_DYNABLOCK, RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi Jim, Sorry about that. Solvate is a command that must have sneaked into the last version. It is used in the ArgusLab molecular dynamics and free energy codes that I run in the research version (I've never released the MD code to end users since I have not figured out a way to make it relatively easy to set up and analyze results). For now, I'd simply ignore the command since the solvent templates are not present in your installation. Cheers, Mark Seattle -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request-.at.-ccl.net]On Behalf Of Jim Kress Sent: Friday, November 19, 2004 8:45 AM To: chemistry-.at.-ccl.net Subject: CCL:Solvate in ArgusLab In the latest version of ArgusLab there is a 'solvate' command under the Tools menu. Anyone know how to use it? When I load a molecule and then issue the solvate command, I get an error message and then the program hangs. Jim -= 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-.at.-ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST-.at.-ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow-.at.-nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+