From chemistry-request@server.ccl.net Wed Jan 23 00:15:05 2002 Received: from portal.gmu.edu ([129.174.0.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0N5F5c04656 for ; Wed, 23 Jan 2002 00:15:05 -0500 Received: from ib3.gmu.edu (ib3.gmu.edu [129.174.206.39]) by portal.gmu.edu (8.8.8/8.8.8) with ESMTP id AAA04879 for ; Wed, 23 Jan 2002 00:14:49 -0500 (EST) Received: from localhost (ivaisman@localhost) by ib3.gmu.edu (SGI-8.9.3/8.9.3) with ESMTP id AAA27297 for ; Wed, 23 Jan 2002 00:09:14 -0500 (EST) Date: Wed, 23 Jan 2002 00:09:14 -0500 From: Iosif Vaisman To: chemistry@ccl.net Subject: CFP: Computational Protein Structure Analysis Workshop Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Workshop on Computational Protein Structure Analysis March 10, 2002 Durham, North Carolina, USA The Workshop on Computational Protein Structure Analysis will be a part of the Fourth Conference on Computational Biology and Genome Informatics that is held in conjunction with several other Joint Conferences on Information Sciences in the Research Triangle Park area of North Carolina. The 6th Joint Conference on Information Sciences (JCIS), scheduled for March 8-14, 2002 will continue a decade-long tradition of offering cutting-edge scientific and technological presentations and discussion. Computational Biology will be one of the major themes at JCIS-2002. The Computational Protein Structure Analysis workshop will bring together academic, governmental and industrial researchers interested in various aspects of theoretical and computational studies of protein structure and protein modelling. The workshop topics include: - Protein structure classification - Protein structure comparison - Protein structure prediction - Structural genomics - Molecular simulation of proteins - Protein modeling Papers describing original research in any of the above listed topics are invited. To submit a paper please email an abstract (not more than one page, plain text or PDF) before February 1, 2002 to Iosif Vaisman (ivaisman@gmu.edu). Acceptance notification will be sent by February 7, 2002. Workshop Co-Chairs: Tom Darden (NIEHS), Alex Tropsha (UNC), Iosif Vaisman (GMU). Additional information and registration forms are available at http://scs-pw.gmu.edu/vaisman/cpsa.html Iosif Vaisman, Ph.D. Associate Professor of Bioinformatics School of Computational Sciences George Mason University, MSN 4E3 Manassas, VA 20110 703.993.8431 (voice), 703.993.8401 (fax), scs-pw.gmu.edu/vaisman (web) From chemistry-request@server.ccl.net Tue Jan 22 11:04:15 2002 Received: from web10004.mail.yahoo.com ([216.136.130.40]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g0MG4EI02329 for ; Tue, 22 Jan 2002 11:04:14 -0500 Message-ID: <20020122160359.83008.qmail@web10004.mail.yahoo.com> Received: from [128.83.164.61] by web10004.mail.yahoo.com via HTTP; Tue, 22 Jan 2002 08:03:59 PST Date: Tue, 22 Jan 2002 08:03:59 -0800 (PST) From: Jacie Subject: need help on "cross-correlated" To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers: I have a question: how to do the "cross-correlated" analysis when a set of experimental values are regressed again the calculated descriptors to generate a model with regression coefficients? Could you introduce some reference articles on "cross-correlated" to me? Thanks a lot for your any advice. Jacie ===== __________________________________________________ Do You Yahoo!? Send FREE video emails in Yahoo! Mail! http://promo.yahoo.com/videomail/ From chemistry-request@server.ccl.net Tue Jan 22 20:25:33 2002 Received: from cascara.uvic.ca (root@[142.104.5.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0N1PXc01865 for ; Tue, 22 Jan 2002 20:25:33 -0500 Received: from unix5.uvic.ca (unix5.uvic.ca [142.104.5.117]) by cascara.uvic.ca (8.11.6/8.11.6) with ESMTP id g0N1PEU106694; Tue, 22 Jan 2002 17:25:14 -0800 Date: Tue, 22 Jan 2002 17:25:14 -0800 (PST) From: Roy Jensen To: chemistry@ccl.net cc: Phillip Matz , , Subject: Re: CCL:question of netiquette In-Reply-To: <000001c1a2f2$772f79f0$1200a8c0@chem.wsu.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I often respond directly to the poster because they are the ones interested; all of CCL does not need to see every reply. On topics that might be of more general interest, I ask the poster to summarize to the CCL. (Read: I am interested in the answer too.) The rules you specified would reverse if the poster decides to post a summary and therefore be difficult to apply. Furthermore, someone responding should expect to take ownership and responsibility of their statements. Legally, an email is no different than a mailed letter. A simpler rule would be: Ownership of a statement is reported in summaries unless the owner explicitly requests to remain anonymous. Roy Jensen On Mon, 21 Jan 2002, Phillip Matz wrote: > How about the following: > > 1) If the original CCL poster explicitly states they will post summaries > then the replier (sp) will take it upon themselves to let the poster > know if it is NOT ok to include their name in the posted summary > (default assumption is to give credit to all posters; i.e. the burden of > desiring and receiving privacy is then up to the person offering their > idea) > > 2) If the original CCL poster does not state they will be posting a > summary then the replier should post to the CCL directly (in which case > they will receive "idea ownership"), but in the event that the replier > communicates with the original poster via private email then the replier > must indicate they desire idea ownership (i.e. the default assumption is > the replier desires privacy) in the event the original poster is > requested to post a summary. > > Yes? No? Suggestions? > > Regards, > > Phil Matz On Mon, 21 Jan 2002, Shobe, Dave wrote: > I have uncertainties about that myself. There is the arguement that people > should get credit for their work/ideas, and there is the argument that > privacy should be respected when the response comes from "person to person" > e-mail. The usual practice on CCL seems to be to include the names, but I'm > not sure that's really the correct thing to do. From chemistry-request@server.ccl.net Tue Jan 22 11:39:34 2002 Received: from argyle.richmond.edu ([141.166.188.18]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0MGdYI03272 for ; Tue, 22 Jan 2002 11:39:34 -0500 Received: from sabrash (lfa221037.richmond.edu [141.166.221.37]) by argyle.richmond.edu (8.11.6/8.11.6) with SMTP id g0MGYYb20915 for ; Tue, 22 Jan 2002 11:34:35 -0500 Message-Id: <3.0.5.32.20020122114455.00815480@facstaff.richmond.edu> X-Sender: sabrash@facstaff.richmond.edu X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Tue, 22 Jan 2002 11:44:55 -0500 To: CHEMISTRY@ccl.net From: "Samuel A. Abrash" Subject: Front End Programs for Gaussian Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi Folks, I'm about to choose a front end program for Gaussian. I'm working on Suns with Solaris. I know that I can use Spartan, GaussView, and other programs as front ends. What I'm interested in hearing is how well those of you who use these are satisfied by their power and performance. I.e., what do you use, are you happy with it, would you recommend it, and why. I'll summarize the responses if and only if I'm requested to, and if I do, I'll give credit to those who communicate with me unless they request that I don't. Best regards, Sam Abrash Samuel A. Abrash Associate Professor Department of Chemistry University of Richmond Richmond, VA 23173 Phone: (804) 289-8248 Fax: (804) 287-1897 E-mail: sabrash@richmond.edu http://www.richmond.edu/~sabrash "Research is to teaching as sin is to confession - if you don't participate in one you don't have anything to say at the other." From chemistry-request@server.ccl.net Tue Jan 22 17:28:32 2002 Received: from web13801.mail.yahoo.com ([216.136.175.11]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g0MMSWI10928 for ; Tue, 22 Jan 2002 17:28:32 -0500 Message-ID: <20020122211202.94819.qmail@web13801.mail.yahoo.com> Received: from [130.108.137.217] by web13801.mail.yahoo.com via HTTP; Tue, 22 Jan 2002 13:12:02 PST Date: Tue, 22 Jan 2002 13:12:02 -0800 (PST) From: Chad Hollingsworth Subject: G98 bond order To: CHEMISTRY@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Greetings, I have performed Mulliken and natural population analysis on the equilibrium geometries of several molecules in Gaussian98. I would like to know bond orders, but am having trouble extracting this information from the output. Any help would be greatly appreciated. Thanks, ===== Chad A. Hollingsworth Research Assistant - Wright State University Department of Chemistry -------------------------------------------------------------------- Office: 466 Oleman Hall Lab: 219 Oelman Hall Hours for P-Chem Assitance: 8-9 am M thru F (or by appointment) -------------------------------------------------------------------- God listens to knee-mails!!! __________________________________________________ Do You Yahoo!? Send FREE video emails in Yahoo! Mail! http://promo.yahoo.com/videomail/ From chemistry-request@server.ccl.net Wed Jan 23 00:03:39 2002 Received: from hermes.cc.utexas.edu ([128.83.40.125]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0N53dc04535 for ; Wed, 23 Jan 2002 00:03:39 -0500 Received: (from www@localhost) by hermes.cc.utexas.edu (8.9.3/8.9.3/cc-webmail.mc-1.3) id XAA11195 for chemistry@ccl.net; Tue, 22 Jan 2002 23:03:23 -0600 (CST) From: clj@mail.utexas.edu To: chemistry@ccl.net Message-ID: <1011762203.3c4e441b33ef3@webmailapp2.cc.utexas.edu> Date: Tue, 22 Jan 2002 23:03:23 -0600 (CST) MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.7 X-Originating-IP: 128.83.128.86 Dear CCLers: I have a question: how to do the "cross-correlated" analysis when a set of experimental values are regressed again the calculated descriptors to generate a model with regression coefficients? Could you introduce some reference articles on "cross-correlated" to me? Thanks a lot for your any advice. Jacie From chemistry-request@server.ccl.net Tue Jan 22 18:12:39 2002 Received: from mail.chem.tamu.edu ([165.91.176.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0MNCcI12939 for ; Tue, 22 Jan 2002 18:12:38 -0500 Received: from [165.91.177.236] (account fan HELO mail.chem.tamu.edu) by mail.chem.tamu.edu (CommuniGate Pro SMTP 3.5.2) with ESMTP id 996646 for chemistry@ccl.net; Tue, 22 Jan 2002 17:05:12 -0600 Sender: fan@ccl.net Message-ID: <3C4E022E.E58C6AC1@mail.chem.tamu.edu> Date: Tue, 22 Jan 2002 18:22:06 -0600 From: Hua-Jun Fan Organization: Texas A&M University X-Mailer: Mozilla 4.77C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: largest system available References: <200201210143.g0L1hqI01669@server.ccl.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, CCLer I am interesting in find out what is the largest system studied using DFT method until now. In another words, assuming one has enomous of CPU power to himself (eg. 512 cpu, 512GB memory, no limit cpu time), what is the largest system has been optimized? Either using commercial software, such as Gaussian or ADF, or freeware, such as MWchem and GAMESS. Any comments will be appreciated! Have a nice day! huajun From chemistry-request@server.ccl.net Tue Jan 22 21:19:52 2002 Received: from jaguar.it.wsu.edu (root@[134.121.0.73]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0N2Jpc02306 for ; Tue, 22 Jan 2002 21:19:51 -0500 Received: from enigma (ucis.chem.wsu.edu [134.121.41.180]) by jaguar.it.wsu.edu (8.12.1/8.12.1) with ESMTP id g0N2JYYd002261; Tue, 22 Jan 2002 18:19:34 -0800 (PST) From: "Phillip Matz" To: "'Roy Jensen'" , Cc: , Subject: RE: CCL:question of netiquette Date: Tue, 22 Jan 2002 18:19:34 -0800 Message-ID: <000e01c1a3b4$65e064d0$1200a8c0@chem.wsu.edu> 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, Build 10.0.3416 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal In-Reply-To: X-Virus-Scanned: by amavisd-milter (http://amavis.org/) > A simpler rule would be: > Ownership of a statement is reported in summaries unless > the owner explicitly requests to remain anonymous. > > Roy Jensen That seems logical to me (far simpler too!). -Phil Matz -----Original Message----- From: Roy Jensen [mailto:royj@uvic.ca] Sent: Tuesday, January 22, 2002 5:25 PM To: chemistry@ccl.net Cc: Phillip Matz; jkl@ccl.net; dshobe@sud-chemieinc.com Subject: Re: CCL:question of netiquette I often respond directly to the poster because they are the ones interested; all of CCL does not need to see every reply. On topics that might be of more general interest, I ask the poster to summarize to the CCL. (Read: I am interested in the answer too.) The rules you specified would reverse if the poster decides to post a summary and therefore be difficult to apply. Furthermore, someone responding should expect to take ownership and responsibility of their statements. Legally, an email is no different than a mailed letter. A simpler rule would be: Ownership of a statement is reported in summaries unless the owner explicitly requests to remain anonymous. Roy Jensen On Mon, 21 Jan 2002, Phillip Matz wrote: > How about the following: > > 1) If the original CCL poster explicitly states they will post > summaries then the replier (sp) will take it upon themselves to let > the poster know if it is NOT ok to include their name in the posted > summary (default assumption is to give credit to all posters; i.e. the > burden of desiring and receiving privacy is then up to the person > offering their > idea) > > 2) If the original CCL poster does not state they will be posting a > summary then the replier should post to the CCL directly (in which > case they will receive "idea ownership"), but in the event that the > replier communicates with the original poster via private email then > the replier must indicate they desire idea ownership (i.e. the default > assumption is the replier desires privacy) in the event the original > poster is requested to post a summary. > > Yes? No? Suggestions? > > Regards, > > Phil Matz On Mon, 21 Jan 2002, Shobe, Dave wrote: > I have uncertainties about that myself. There is the arguement that > people should get credit for their work/ideas, and there is the > argument that privacy should be respected when the response comes from > "person to person" e-mail. The usual practice on CCL seems to be to > include the names, but I'm not sure that's really the correct thing to > do. From chemistry-request@server.ccl.net Tue Jan 22 22:22:56 2002 Received: from hotmail.com ([64.4.9.186]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0N3Muc03453 for ; Tue, 22 Jan 2002 22:22:56 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 22 Jan 2002 19:22:35 -0800 Received: from 129.82.76.225 by lw9fd.law9.hotmail.msn.com with HTTP; Wed, 23 Jan 2002 03:22:35 GMT X-Originating-IP: [129.82.76.225] From: "Elena Jakubikova" To: chemistry@ccl.net Subject: linearly dependent basis set or the mystery of the large alpha MO Date: Tue, 22 Jan 2002 20:22:35 -0700 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 23 Jan 2002 03:22:35.0603 (UTC) FILETIME=[33C8D230:01C1A3BD] Dear CClers, I would like to learn more about the problem of nearly linearly dependent basis set and very large MO coefficients that arise thanks to this problem. I have read in the Gaussian manual that these large coefficients may lead to subtantial numerical errors and that in case any MO is larger than 1000, the calculation is aborted. Does any of you have an idea how big these numerical errors might be if my largest MO is of the order 100? When do I really need to start worry about numerical accuracy of the calculation, at which value of the largest MO coefficient? And finally, how does Gaussian program deal with the problem of very large coefficients, is it trying to correct the problem in any way (for example by excluding certain basis functions > from further calculation) or it just continues calculation irrespectively of what the error might be on the end? I also tried to learn some more about this problem from the literature, but I was not very successful. The only paper touching this problem I found was 'A. Wallis, D.L.S. McElwain, H.O. Pritchard, "Variation method and the algebraic eigenvalue problem.", Int.J.Quantum Chem. 3(5), 711-722 (1969).' Does anybody know where can I find some more information about this? Thank you very much for your help! Elena -------------------------- Elena Jakubikova graduate student Department of Chemistry Colorado State University _________________________________________________________________ Send and receive Hotmail on your mobile device: http://mobile.msn.com From chemistry-request@server.ccl.net Wed Jan 23 04:08:03 2002 Received: from mail2.zrz.tu-berlin.de ([130.149.4.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0N982c10627 for ; Wed, 23 Jan 2002 04:08:02 -0500 Received: from mailszrz.zrz.tu-berlin.de ([130.149.4.11]) by mail2.zrz.tu-berlin.de with esmtp (exim-3.34) id 16TJNd-0007A5-00; Wed, 23 Jan 2002 10:07:41 +0100 Received: from natrium.chem.tu-berlin.de ([130.149.169.143]) by mailszrz.zrz.tu-berlin.de with esmtp (exim-3.34) id 16TJNc-0002a9-00; Wed, 23 Jan 2002 10:07:40 +0100 Mime-Version: 1.0 X-Sender: chwu0531@mailszrz.zrz.tu-berlin.de Message-Id: In-Reply-To: <3C4E022E.E58C6AC1@mail.chem.tamu.edu> References: <200201210143.g0L1hqI01669@server.ccl.net> <3C4E022E.E58C6AC1@mail.chem.tamu.edu> Date: Wed, 23 Jan 2002 10:07:40 +0100 To: Hua-Jun Fan From: Christoph van =?iso-8859-1?Q?W=FCllen?= Subject: Re: CCL:largest system available Cc: chemistry@ccl.net Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g0N983c10628 >Hi, CCLer > >I am interesting in find out what is the largest system studied >using DFT method until now. In another words, assuming one has >enomous of CPU power to himself (eg. 512 cpu, 512GB memory, no >limit cpu time), what is the largest system has been optimized? The issue might be, what is the largest system where a geometry optimization makes sense. +---------------------------------+----------------------------------+ | Prof. Christoph van Wüllen | Tele-Phone (+49) (0)30 314 27870 | | Technische Universität Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 | | Straße des 17. Juni 135 | eMail | | D-10623 Berlin, Germany | Christoph.vanWullen@TU-Berlin.De | +---------------------------------+----------------------------------+ -- From chemistry-request@server.ccl.net Wed Jan 23 05:13:40 2002 Received: from dep.chem.rug.nl ([129.125.7.81]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0NADec12077 for ; Wed, 23 Jan 2002 05:13:40 -0500 Received: from [129.125.7.13] (theochem1.chem.rug.nl [129.125.7.13]) by dep.chem.rug.nl (8.9.3/8.9.3/Debian 8.9.3-21) with ESMTP id LAA17002; Wed, 23 Jan 2002 11:13:20 +0100 X-Authentication-Warning: dep.chem.rug.nl: Host theochem1.chem.rug.nl [129.125.7.13] claimed to be [129.125.7.13] Mime-Version: 1.0 X-Sender: swart@hydra.chem.rug.nl Message-Id: In-Reply-To: <3C4C3E63.6080405@vub.ac.be> References: <3C4C3E63.6080405@vub.ac.be> Date: Wed, 23 Jan 2002 11:13:18 +0100 To: Pierre Mignon From: Marcel Swart Subject: Re: CCL:FF, and QM/MM Software Content-Type: text/plain; charset="us-ascii" ; format="flowed" >Hello everybody, >I am interested to buy a software to do QM/MM calcculations and FF >minimalisations for a project concerning biochemistry. I know some >about CHARMM or AMBER, but I have never use them. Could anybody give >me suggestions and critics upon their use and also on other software >? >Thank's in advance. >Pierre Mignon . QM/MM calculations on biochemical systems are possible with ADF, and have been applied already to systems of 2000-13000 atoms, where the AMBER95 force field is used for the MM system. -- Marcel Swart Theoretische Chemie (MSC) / Moleculaire Dynamica (GBB) Rijksuniversiteit Groningen Nijenborgh 4 9747 AG Groningen The Netherlands m.swart@chem.rug.nl http://go.to/m.swart From chemistry-request@server.ccl.net Wed Jan 23 06:46:41 2002 Received: from as1200.organik.uni-erlangen.de ([131.188.128.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0NBkec14375 for ; Wed, 23 Jan 2002 06:46:41 -0500 Received: from chemie.uni-erlangen.de (excelsior.chemie.uni-erlangen.de [131.188.128.76]) by as1200.organik.uni-erlangen.de (8.8.7/8.1.11-FAU) with ESMTP id MAA04859 for ; Wed, 23 Jan 2002 12:46:37 +0100 (MET) Sender: Harald.Lanig@Organik.Uni-Erlangen.DE Message-ID: <3C4EA29C.ED7E9341@chemie.uni-erlangen.de> Date: Wed, 23 Jan 2002 12:46:36 +0100 From: Harald Lanig Organization: Computer-Chemie-Centrum X-Mailer: Mozilla 4.76C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Announcement: Beilstein Workshop Bozen 2002 - Molecular Informatics Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear list members, I am posting the following announcement on behalf of Martin Hicks, Beilstein-Institut, Frankfurt/Main, Germany ---------- International Workshop - Molecular Informatics ---------- Apologies for any cross-postings We would like to inform you about our forthcoming workshop: Molecular Informatics: Confronting Complexity May 13th-16th, 2002, Bozen, Italy. This workshop will address the new challenges that now face scientists in the post-genome era - in particular, the integration of two, until recently, disparate sciences, i.e. cheminformatics and bioinformatics. It is now essential to bridge the gap between chemists, dealing with the intricacies of drug discovery, and biologists, working with complex cell physiological systems, in order to make any real and significant advances in the areas of molecular structure-function relationships and drug-target specificity. Speakers have been asked to bear in mind the interdisciplinary nature of the workshop, and where applicable, to address some of the fundamental issues in molecular informatics that are seldom discussed and still require to be effectively solved. The following themes will be covered: knowledge discovery and data mining, rational drug design, prediction of small molecule bioavailability (ADMETox) properties, protein structure and function determination, new methods of drug-target modeling, cellular metabolism, and the use of high-throughput methods (biochips) for acquiring gene expression and protein binding information. The workshop will take place in the historic Hotel Schloss Korb. The setting and the limited number of participants (ca. 50-60), provide a very convivial atmosphere for the ready exchange of thoughts and ideas. We have an excellent line-up of speakers including: Karl-Heinz Baringhaus, Aventis Hans-Joachim Böhm, Hoffmann-LaRoche Timothy Clark, University of Erlangen-Nürnberg Athel Cornish-Bowden, CNRS-BIP Luc De Raedt, University of Freiburg Chris Dobson, University of Cambridge Richard Goldstein, University of Michigan Jörg Hoheisel, German Cancer Research Center Kevin Holme, Lion Bioscience Harren Jhoti, Astex Technology Peter Johnson, University of Leeds William Jorgensen, Yale University Carsten Kettner, Beilstein-Institut Christopher Lipinski, Pfizer Global Research and Development Gerald Maggiora, Pharmacia Friedhelm Pfeiffer, MPI of Biochemistry Graham Richards, University of Oxford Brian Shoichet, Northwestern University Jeffrey Skolnick, Donald Danforth Plant Science Center Shoshana Wodak, Université Libre de Bruxelles Please visit our web-site www.beilstein-institut.de for more information about the workshop, the scientific program and the registration form. We hope very much that you would be interested in attending. Places at the workshop are limited and will be allocated on a first-come basis. Further information will be sent in circulars well before the workshop. If you have any questions, please do not hesitate to get in touch. Best regards, Martin Hicks Carsten Kettner Wolfgang Koerner ------------------------------------------------------------- Dr. Martin G. Hicks Head of Funding Division, Symposia Beilstein-Institut Varrentrappstr. 40-42 60486 Frankfurt Germany Tel: +49 (0)69 7917 426; Fax: +49 (0)69 7917 473 mhicks@beilstein-institut.de ------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Jan 23 06:44:08 2002 Received: from hotmail.com ([64.4.37.120]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0NBi7c14307; Wed, 23 Jan 2002 06:44:07 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Wed, 23 Jan 2002 03:43:46 -0800 Received: from 133.11.92.210 by pv2fd.pav2.hotmail.msn.com with HTTP; Wed, 23 Jan 2002 11:43:46 GMT X-Originating-IP: [133.11.92.210] From: "tianxiao young" To: chemistry-request@ccl.net Cc: chemistry@ccl.net, nwchem-support@emsl.pnl.gov Subject: nwchem Date: Wed, 23 Jan 2002 11:43:46 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 23 Jan 2002 11:43:46.0823 (UTC) FILETIME=[37A0D970:01C1A403] Dear NW Chem users and CCLers: Does anyone know how to do the "relativistic" ab initio MD calculations using the NWChem program? Can I produce the relativistic pseudopotential using pspw? Any kind of help is appreciated. Thanks in advance. young The University of Tokyo _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp. From chemistry-request@server.ccl.net Wed Jan 23 09:13:08 2002 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0NED6c18135 for ; Wed, 23 Jan 2002 09:13:07 -0500 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 16TO69-0002Bw-00 for CHEMISTRY@ccl.net; Wed, 23 Jan 2002 14:09:57 +0000 Date: Wed, 23 Jan 2002 14:09:56 +0000 (GMT) From: Szilveszter Juhos To: CHEMISTRY@ccl.net Subject: Conformation representation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear List Memebers, Is there a compact, unambigous and unique representation of 3D structure of a molecule apart from listing all the coordinates and atom types etc in rows? Unique in that sense that there is only one possible representation for a particular conformation of a molecule (AFAIK Z matrix is not neccessarily is like this, there can be different Z matrices for the same molecule). I am thinking about something like SMILES but with 3D information in it. Thanks: Szilva From chemistry-request@server.ccl.net Wed Jan 23 11:32:51 2002 Received: from ccmsi.jsums.edu ([143.132.103.54]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0NGWpc21789 for ; Wed, 23 Jan 2002 11:32:51 -0500 Received: from ccmsi.jsums.edu [10.30.3.44] by ccmsi.jsums.edu with ESMTP (SMTPD32-7.05) id A5A41E800D2; Wed, 23 Jan 2002 10:32:36 -0600 Message-ID: <3C4EE5A1.6EC0888A@ccmsi.jsums.edu> Date: Wed, 23 Jan 2002 10:32:33 -0600 From: "Dr. Giju Thomas Kalathingal" Organization: Jackson State University X-Mailer: Mozilla 4.77 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: Hua-Jun Fan , chemistry@ccl.net Subject: Re: CCL:largest system available References: <200201210143.g0L1hqI01669@server.ccl.net> <3C4E022E.E58C6AC1@mail.chem.tamu.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hua-Jun Fan wrote: > Hi, CCLer > > I am interesting in find out what is the largest system studied > using DFT method until now. In another words, assuming one has > enomous of CPU power to himself (eg. 512 cpu, 512GB memory, no > limit cpu time), what is the largest system has been optimized? > Either using commercial software, such as Gaussian or ADF, or > freeware, such as MWchem and GAMESS. Any comments will be > appreciated! > What do you meany by largest? Is it the molecule, theoretical method, basis sets,......? Largest systems depends clearly on these factors. If you look curiously, you will find even hydrogen molecule is largest:) Any comments? Giju Kalathingal From chemistry-request@server.ccl.net Wed Jan 23 11:13:30 2002 Received: from gate3.oss.akzonobel.nl ([192.87.3.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0NGDTc21355 for ; Wed, 23 Jan 2002 11:13:30 -0500 Received: (from fwmaster@localhost) by gate3.oss.akzonobel.nl (8.9.1a/8.6.12) id RAA15456 for ; Wed, 23 Jan 2002 17:13:04 +0100 (MET) Received: by gate3.oss.akzonobel.nl via smap (V1.3) id sma014446; Wed, 23 Jan 02 17:11:47 +0100 Received: by ras1.oss.akzonobel.nl with Internet Mail Service (5.5.2653.19) id ; Wed, 23 Jan 2002 17:11:47 +0100 Message-ID: From: "Wagener, M. (Markus)" To: "'CHEMISTRY@ccl.net'" Subject: Reminder - 6th International Conference on Chem Structures, The N etherlands Date: Wed, 23 Jan 2002 17:11:44 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" This important triannual conference will take place on June 2 - 6, 2002, at the beautiful conference center in Noordwijkerhout, The Netherlands. Please visit the conference's website at http://www.chemweb.com/docs/6iccs/6iccs.html for the 'Call for Papers' and other details. Please also notice the rapidly approaching deadlines for: o paper submissions (February 15th) o early registration (March 1) Markus Wagener -- ----------------------------------------------------------- Dr. Markus Wagener NV Organon MDI-CMC RK2330 phone: +31-412-661380 P.O. Box 20 FAX: +31-412-662539 5340 BH Oss Email: markus.wagener@organon.com The Netherlands ----------------------------------------------------------- -------------------------------------------------------------------- This message, including attached files, may contain confidential information and is intended only for the use by the individual and/or the entity to which it is addressed. Any unauthorized use, dissemination of, or copying of the information contained herein is not allowed and may lead to irreparable harm and damage for which you may be held liable. If you receive this message in error or if it is intended for someone else please notify the sender by returning this e-mail immediately and delete the message. -------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Jan 23 11:01:36 2002 Received: from salmon.maths.tcd.ie (mmdf@[134.226.81.11]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g0NG1ac21130 for ; Wed, 23 Jan 2002 11:01:36 -0500 Received: from walton.maths.tcd.ie by salmon.maths.tcd.ie with SMTP id ; 23 Jan 2002 16:01:20 +0000 (GMT) Date: Wed, 23 Jan 2002 16:01:20 +0000 (GMT) From: Gemma Kinsella To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I'm trying to run some molecular dynamics simualtions on a protein/drug interaction. Does anyone know of any free packages available to do this? I've been having some problems with Dl_poly/Dlprotein. Thanks, Gemma From chemistry-request@server.ccl.net Wed Jan 23 10:14:39 2002 Received: from mail-b.bcc.ac.uk ([144.82.100.22]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0NFEcc20010 for ; Wed, 23 Jan 2002 10:14:38 -0500 Received: from socrates-a.ucl.ac.uk by mail-b.bcc.ac.uk with SMTP (Mailer) with ESMTP; Wed, 23 Jan 2002 15:13:47 +0000 Received: (from uccatvm@localhost) by socrates-a.ucl.ac.uk (8.10.2+Sun/8.9.3) id g0NFDlN00482; Wed, 23 Jan 2002 15:13:47 GMT From: uccatvm Message-Id: <200201231513.g0NFDlN00482@socrates-a.ucl.ac.uk> Subject: Re: CCL:linearly dependent basis set or the mystery of the large alpha MO To: chemistry@ccl.net Date: Wed, 23 Jan 2002 15:13:46 +0000 (GMT) Cc: T.vanMourik@ucl.ac.uk (Tanja van Mourik) In-Reply-To: from "Elena Jakubikova" at Jan 22, 2002 08:22:35 PM X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Elena, > I would like to learn more about the problem of nearly linearly > dependent basis set and very large MO coefficients that arise thanks > to this problem. I have read in the Gaussian manual that these large > coefficients may lead to subtantial numerical errors and that in case > any MO is larger than 1000, the calculation is aborted. Does any of > you have an idea how big these numerical errors might be if my largest > MO is of the order 100? When do I really need to start worry about > numerical accuracy of the calculation, at which value of the largest > MO coefficient? And finally, how does Gaussian program deal with the > problem of very large coefficients, is it trying to correct the > problem in any way (for example by excluding certain basis functions > > from further calculation) or it just continues calculation > irrespectively of what the error might be on the end? Gaussian deletes eigenvectors of the overlap matrix belonging to small eigenvalues (threshold value 10E-5). You may want to read David Feller's messages to CCL on this subject: see CCL archive of Jan 21, 2000. In my experience, you have to really careful if you compare energies obtained with different programs, as these may have different threshold values for deleting the eigenvectors. Feller reports an energy difference of more than 4 millihartree for Ar computed with G98 and other programs that do not delete almost linearly dependent functions. > > I also tried to learn some more about this problem from the > literature, but I was not very successful. The only paper touching > this problem I found was 'A. Wallis, D.L.S. McElwain, H.O. Pritchard, > "Variation method and the algebraic eigenvalue problem.", > Int.J.Quantum Chem. 3(5), 711-722 (1969).' Does anybody know where can > I find some more information about this? I encountered problems with almost linearly dependent functions with basis sets containing large sets of bondfunctions: see T. van Mourik, R.J. Vos, J.H. van Lenthe and F.B. van Duijneveldt, Int. J. Quant. Chem. 63, 805 (1997). It is a bit of a special case, but it may be of interest if you want to learn more about this subject. Hope this of any use to you, Tanja -- ===================================================================== Tanja van Mourik Royal Society University Research Fellow Chemistry Department University College London phone: +44 (0)20-7679-4663 20 Gordon Street e-mail: work: T.vanMourik@ucl.ac.uk London WC1H 0AJ, UK home: tanja@netcomuk.co.uk http://www.chem.ucl.ac.uk/people/vanmourik/index.html ===================================================================== From chemistry-request@server.ccl.net Wed Jan 23 11:23:30 2002 Received: from salmon.maths.tcd.ie (mmdf@[134.226.81.11]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g0NGNTc21631 for ; Wed, 23 Jan 2002 11:23:30 -0500 Received: from walton.maths.tcd.ie by salmon.maths.tcd.ie with SMTP id ; 23 Jan 2002 16:23:13 +0000 (GMT) Date: Wed, 23 Jan 2002 16:23:13 +0000 (GMT) From: Gemma Kinsella To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi again, Does anybody have a list of the atom type labels for the gromos force field. It would be a great help. Thanks, Gemma From chemistry-request@server.ccl.net Wed Jan 23 14:52:27 2002 Received: from mail-01.med.umich.edu ([141.214.93.149]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0NJqRc28522 for ; Wed, 23 Jan 2002 14:52:27 -0500 Received: from gwia-01-MTA by mail-01.med.umich.edu with Novell_GroupWise; Wed, 23 Jan 2002 14:52:09 -0500 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.1 Date: Wed, 23 Jan 2002 14:51:53 -0500 From: "Renxiao Wang" To: Subject: about solvation energy and SAS method Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g0NJqRc28523 Dear CCLers, It looks to me that all the solvent-accessible surface methods for computing solvation (hydration) energies so far, including the SA part in PB/SA and GB/SA, are calibrated through only a handful of organic compounds with measured solvation energies. So my question is: has anybody derived or applied or tested SAS methods (including PB/SA or GB/SA) on a *large* collection of organic compounds with known solvation energies? I hope I have not missed any important work in this area. Any idea? I will put back the summary! Have a good day, Renxiao Wang, Ph.D. University of Michigan Medical School From chemistry-request@server.ccl.net Wed Jan 23 14:32:13 2002 Received: from mtiwmhc22.worldnet.att.net ([204.127.131.47]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0NJWDc27983 for ; Wed, 23 Jan 2002 14:32:13 -0500 Received: from puter ([138.23.156.82]) by mtiwmhc22.worldnet.att.net (InterMail vM.4.01.03.27 201-229-121-127-20010626) with ESMTP id <20020123193151.XMLR1006.mtiwmhc22.worldnet.att.net@puter> for ; Wed, 23 Jan 2002 19:31:51 +0000 Message-ID: <000801c1a402$3c599c00$01000001@puter> From: "Donald Keidel" To: Subject: g98: installation linux Date: Wed, 23 Jan 2002 11:36:41 -0000 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0005_01C1A402.3A4EFEF0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0005_01C1A402.3A4EFEF0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello all, Does anyone know of a good set of notes on the web or personal that = describes how to install gaussian 98 on a linux machine (i am running = redHat 7.2). Thank you in advance for the help. Don --------------------------------------------------- Donald J. Keidel University of California, Riverside Department of Biochemistry and Molecular Biology Riverside, CA 92521 phone: (909) 787-5493 fax: (909) 787-4434 dkeidel397@att.net webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm ------=_NextPart_000_0005_01C1A402.3A4EFEF0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello all,
 
Does anyone know of a good set of notes = on the web=20 or personal that describes how to install gaussian 98 on a linux machine = (i am=20 running redHat 7.2).  Thank you in advance for the = help.
 
Don
---------------------------------------------------
Donald = J.=20 Keidel
University of California, Riverside
Department of = Biochemistry and=20 Molecular Biology
Riverside, CA 92521
phone:  (909)=20 787-5493
fax:  (909) 787-4434
dkeidel397@att.net
webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm<= BR>
------=_NextPart_000_0005_01C1A402.3A4EFEF0-- From chemistry-request@server.ccl.net Wed Jan 23 14:51:15 2002 Received: from mailrelay1.lrz-muenchen.de ([129.187.254.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0NJpFc28480 for ; Wed, 23 Jan 2002 14:51:15 -0500 Received: from sun3.lrz-muenchen.de by mailrelay1.lrz-muenchen.de with ESMTP for chemistry@ccl.net; Wed, 23 Jan 2002 20:50:38 +0100 Received: from localhost (ui22204@localhost) by sun3.lrz-muenchen.de (8.8.8+Sun/8.8.8) with ESMTP id UAA07289 for ; Wed, 23 Jan 2002 20:50:36 +0100 (MET) X-Authentication-Warning: sun3.lrz-muenchen.de: ui22204 owned process doing -bs Date: Wed, 23 Jan 2002 20:50:36 +0100 (MET) From: Eugene Leitl X-X-Sender: To: Subject: FYI:/. linux desktop clustering Message-Id: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII http://slashdot.org/articles/02/01/22/1854218.shtml "A Linux cluster on the desktop--Rocket Calc just announced their 8- processor "personal" cluster in a mid-tower-sized box. Starting at $4500, you get 8 Celeron 800MHz processors, each with 256MB RAM and a 100Mbps ethernet connection. The box also has an integrated 100Mbps switch. Plus it's sexy." Perhaps less sexy, but for a lot less money, you can also run a cluster of Linux (virtual) machines on your desktop on middle-of-the-road hardware. See this followup on Grant Gross's recent piece on Virtual Machines over at Newsforge. More details at http://www.rocketcalc.com/index.php?loc=redstone