From chemistry-request@ccl.net Wed Mar 24 03:13:43 2004 Received: from wn1.sci.kun.nl (wn1.sci.kun.nl [131.174.8.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2O8Dgjs019979 for ; Wed, 24 Mar 2004 03:13:42 -0500 Received: from ac12.sci.kun.nl [131.174.179.19] (helo=ac12.sci.kun.nl) by wn1.sci.kun.nl (8.12.10/3.67) with ESMTP id i2O8GO26028236; Wed, 24 Mar 2004 09:16:24 +0100 (MET) From: "E.L. Willighagen" Reply-To: egonw/at/sci.kun.nl Subject: CCL: ANN: virtual lecture on Automatic Virtual Screening Systems Date: Wed, 24 Mar 2004 09:16:23 +0100 User-Agent: KMail/1.5.4 To: CHEMISTRY/at/ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Content-Disposition: inline Message-Id: <200403240916.23792.egonw/at/sci.kun.nl> X-Spam-Status: No, hits=0.0 required=7.0 tests=none 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 members, We are pleased to present the following seminar with audio on the eCheminfo Hub which is available for viewing and discussion March 23-30. Please signup/log into http://conferences.metalayer.net/echeminfo/ to attend and ask your questions. An Automatic Virtual Screening System, John Irwin and Brian K. Shoichet, UCSF Notwithstanding well-known algorithmic weaknesses, molecular docking screens have had important successes in recent years, and are now the most practical technique to leverage structure for ligand discovery. Unfortunately, barriers to entry have largely restricted the techniques to experts and their collaborators. Docking databases are expensive to acquire, require considerable manipulation, and the software is byzantine. Many pitfalls await the unwary docker, such as the preparation of the protein binding site and the choice of dozens of parameters. This has diminished the impact of the technique and limited the sorts of problems to which it can be applied. To address this situation we are building tools and databases that will bring docking to a broad audience, in the spirit of BLAST, and allow its application to new questions. This talk will describe the development of and experience with an early prototype of an automated web-based docking system and its components. We will illustrate some of the strengths and weaknesses of this approach against targets of current or recent therapeutic interest. Barry Hardy, PhD +41 61 851 0170 (office) +41 79 755 2340 (mobile) Email: barry.hardy/at/tiscalinet.ch From chemistry-request@ccl.net Tue Mar 23 17:09:55 2004 Received: from fujitsu1.fujitsu.com (fujitsu1.fujitsu.com [192.240.0.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2NM9sjs005322 for ; Tue, 23 Mar 2004 17:09:54 -0500 Received: from fujitsu1.fujitsu.com (localhost [127.0.0.1]) by fujitsu1.fujitsu.com (8.12.10/8.12.9) with ESMTP id i2NMChAI019685 for ; Tue, 23 Mar 2004 14:12:43 -0800 (PST) Received: from fnanic.fujitsu.com ([133.164.253.1]) by fujitsu1.fujitsu.com (8.12.10/8.12.9) with ESMTP id i2NMCgVh019667 for ; Tue, 23 Mar 2004 14:12:42 -0800 (PST) Received: from cachemai2.fnanic.fujitsu.com (localhost [127.0.0.1]) by fnanic.fujitsu.com (8.12.11/8.12.11) with ESMTP id i2NMCZJQ023807; Tue, 23 Mar 2004 14:12:36 -0800 (PST) Received: from DAVEG-LIFEBOOK.cachesoftware.com (localhost [127.0.0.1]) by cachemai2.fnanic.fujitsu.com (8.12.11/8.12.11) with ESMTP id i2NMKugA011116; Tue, 23 Mar 2004 14:21:01 -0800 (PST) Message-Id: <6.0.3.0.0.20040323140506.01ebd3f8@133.164.253.30> X-Sender: dgallagher@133.164.253.30 (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 6.0.3.0 Date: Tue, 23 Mar 2004 14:12:16 -0800 To: chemistry$at$ccl.net From: David Gallagher Subject: CCL: MOPAC PM5 Accuracy Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_19988201==.ALT" X-Spam-Status: No, hits=0.0 required=7.0 tests=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 --=====================_19988201==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed For those folks who have inquired about references regarding the new MOPAC PM5 method, the author has just published an article comparing the accuracy of PM5 with various other methods for heats of formation. Comparison of the accuracy of semiempirical and some DFT methods for predicting heats of formation, James J. P. Stewart, J Mol Model (2004) 10:6-12 http://www.springerlink.com/app/home/contribution.asp?wasp=m5nhpgquxmjmme2jqjft&referrer=parent&backto=searcharticlesresults,1,2;journal,1,1;linkingpublicationresults,id:100529,1 There is further information in the on-line manual at http://www.cachesoftware.com/techsupport/mopac/ David Gallagher, CAChe Group, Fujitsu --=====================_19988201==.ALT Content-Type: text/html; charset="us-ascii" For those folks who have inquired about references regarding the new MOPAC PM5 method, the author has just published an article comparing the accuracy of PM5 with various other methods for heats of formation.

Comparison of the accuracy of semiempirical and some DFT methods for
predicting heats of formation, James J. P. Stewart, J Mol Model (2004) 10:6-12

http://www.springerlink.com/app/home/contribution.asp?wasp=m5nhpgquxmjmme2jqjft&referrer=parent&backto=searcharticlesresults,1,2;journal,1,1;linkingpublicationresults,id:100529,1

There is further information in the on-line manual at http://www.cachesoftware.com/techsupport/mopac/


David Gallagher, CAChe Group, Fujitsu
--=====================_19988201==.ALT-- From chemistry-request@ccl.net Tue Mar 23 19:29:23 2004 Received: from watusi.nmrfam.wisc.edu (watusi.nmrfam.wisc.edu [144.92.4.140]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2O0TMjs008871 for ; Tue, 23 Mar 2004 19:29:22 -0500 Received: from watusi.nmrfam.wisc.edu (localhost [127.0.0.1]) by watusi.nmrfam.wisc.edu (SGI-8.12.5/8.12.5) with ESMTP id i2O0W6be294238; Tue, 23 Mar 2004 18:32:06 -0600 (CST) Received: from localhost (fuzery@localhost) by watusi.nmrfam.wisc.edu (SGI-8.12.5/8.12.5/Submit) with ESMTP id i2O0Voj4292998; Tue, 23 Mar 2004 18:32:01 -0600 (CST) Date: Tue, 23 Mar 2004 18:31:50 -0600 From: Anna Fuezery To: chemistry$at$ccl.net cc: fuzery$at$nmrfam.wisc.edu Subject: broken symmetry calculations using DFT methods Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=none 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 everyone, I would like to carry out some broken symmetry calculations on di-iron clusters using DFT methods and the Gaussian program. I have searched for articles on this subject, and although I have found many none seem to describe the practical aspects of how to do such calculations (eg. keywords to include in the input file). Do I just include the Guess=Mix keywords in the route section or do I need to add anything else? Furthermore, can I still use this option for di-iron clusters where one of the irons has been reduced (the Gaussian manual says the Guess=Mix keywords are for producing wavefunctions for singlet states and a reduced di-iron cluster would not fall in this category)? Any help is appreciated. Thanks, Anna Fuzery University of Wisconsin - Madison Department of Biochemistry - John Markley Lab 433 Babcock Dr. Madison, WI 53706-1544 (608) 262-4687 ext. 3118 fuzery$at$nmrfam.wisc.edu From chemistry-request@ccl.net Wed Mar 24 12:16:31 2004 Received: from sandmail01.sd.accelrys.com (fw1.sd.accelrys.com [209.120.169.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2OHGSjs006647 for ; Wed, 24 Mar 2004 12:16:28 -0500 To: chminf-l!at!listserv.indiana.edu, chemistry!at!server.ccl.net, qsar_society!at!accelrys.com Subject: Call for Posters - 15th EuroQSAR 2004 MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.5.1 January 21, 2004 Message-ID: From: Osman F Guner Date: Wed, 24 Mar 2004 09:19:19 -0800 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.0.2CF1|June 9, 2003) at 03/24/2004 09:19:21, Serialize complete at 03/24/2004 09:19:21 Content-Type: multipart/alternative; boundary="=_alternative 005EC3D588256E61_=" X-Spam-Status: No, hits=0.0 required=7.0 tests=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 multipart message in MIME format. --=_alternative 005EC3D588256E61_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable If there is only one meeting you can participate this year, EuroQSAR 2004=20 is it.=20 A heritage event with 25 year history, this year's EuroQSAR is unique in=20 that it will also celebrate the 40th anniversary of QSAR. The monumental=20 Hansch-Fujita paper of 1964 (one of the most cited papers) is generally=20 accepted as the beginning of QSAR. Prof. Corwin Hansch has agreed to give = the opening lecture entitled "40 Years with QSAR". The social program=20 takes advantage of the unique aspects of the venue, Istanbul, excursion=20 with cruise at Bosporus and cultural evening with dinner, all included as=20 part of the registration.=20 The organizing committee is putting together a strong technical program=20 under the session headings: QSAR, Chemical Properties (QSPR), Chemistry=20 and Biology Interface, Combinatorial Chemistry, Computer Aided Drug=20 Design, and a surprise new additional session entitled "Emerging=20 Technologies" that will include very new ideas and approaches in the field = that has not been published yet. CALL FOR POSTERS: The single track meeting has limited slots available for oral=20 presentations. The standard format for submitting abstracts for this=20 meeting is POSTERS ! Apart from the invited plenary lecturers, very few poster presenters will=20 be selected by the organizing committee and be invited to change their=20 presentation format to oral communication of 25 minutes presentation=20 followed by 5 minutes Q&A. Peer-reviewed and selected best 30 accepted=20 posters will be offered for publication in the Journal of QSAR and=20 Combinatorial Science. Also, a grant of Euro 1,000.- will be awarded to=20 the top young-investigator (graduate student or postdoc of 30 years or=20 younger) who is presenting a poster. The deadline for submitting posters is May 15th. For more information on=20 how to submit a poster and formats etc., please check the Web-site=20 (http://www.euro-qsar2004.org/).=20 Mark your calendar for this scientific event of the year! EuroQSAR 2004 - = September 5-10, Istanbul, Turkey On behalf of the organizing committee, I am inviting you to submit an=20 abstract for this meeting. Regards...Osman Osman F. G=FCner, Ph.D. Executive Director Cheminformatics and Rational Drug Design Accelrys Inc., 858-799-5341 osman!at!accelrys.com, http://www.accelrys.com --=_alternative 005EC3D588256E61_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
If there is only one meeting you can participate this year, EuroQSAR 2004 is it.

A heritage event with 25 year histor= y, this year's EuroQSAR is unique in that it will also celebrate the 40th anniversary of QSAR.  The monumental Hansch-Fujita paper of 1964 (one of the most cited papers) is generally accepted as the beginning of QSAR.  Prof. Corwin Hansch has agreed to give the opening lecture entitled "40 Years with QSAR".  The social program takes advantage of the unique aspects of the venue, Istanbul, excursion with cruise at Bosporus and cultural evening with dinner, all included as part of the registration.  

The organizing committee is putting together a strong technical program under the session headings: QSAR, Chemi= cal Properties (QSPR), Chemistry and Biology Interface, Combinatorial Chemistry, Computer Aided Drug Design, and a surprise new additional session entitled "Emerging Technologies" that will include very new ideas and approaches in the field that has not been published yet.

CALL FOR POSTERS:

The single track meeting has limited slots available for oral presentations.  The standard format for submi= tting abstracts for this meeting is POSTERS !

Apart from the invited plenary lectu= rers, very few poster presenters will be selected by the organizing committee and be invited to change their presentation format to oral communication of 25 minutes presentation followed by 5 minutes Q&A.  Peer-review= ed and selected best 30 accepted posters will be offered for publication in the Journal of QSAR and Combinatorial Science.  Also, a grant of Euro 1,000.- will be awarded to the top young-investigator (graduate student or postdoc of 30 years or younger) who is presenting a poster.

The deadline for submitting posters is May 15th.  For more information on how to submit a poster and forma= ts etc., please check the Web-site (http://www.euro-qsar2004.org/).  

Mark your calendar for this scientif= ic event of the year!  EuroQSAR 2004 - September 5-10, Istanbul, Turkey

On behalf of the organizing committe= e, I am inviting you to submit an abstract for this meeting.

Regards...Osman

Osman F. G=FCner, Ph.D.
Executive Director
Cheminformatics and Rational Drug Design
Accelrys Inc.,  858-799-5341
osman!at!accelrys.com, http://www.accelrys.com --=_alternative 005EC3D588256E61_=-- From chemistry-request@ccl.net Wed Mar 24 10:08:59 2004 Received: from relay.uni-heidelberg.de (relay.uni-heidelberg.de [129.206.100.212]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2OF8vjs002876 for ; Wed, 24 Mar 2004 10:08:58 -0500 Received: from euklid.pci.uni-heidelberg.de (euklid.pci.uni-heidelberg.de [129.206.21.104]) by relay.uni-heidelberg.de (8.12.10/8.12.10) with ESMTP id i2OFBkiv004669 for ; Wed, 24 Mar 2004 16:11:49 +0100 (MET) Received: from bernd by euklid.pci.uni-heidelberg.de with local (Exim 3.35 #1 (Debian)) id 1B6A2i-0006ow-00 for ; Wed, 24 Mar 2004 16:11:44 +0100 From: Bernd Schubert Subject: Fwd: [Beowulf] 64-bit Gaussian 03 on Opteron/SuSE Date: Wed, 24 Mar 2004 16:11:31 +0100 User-Agent: KMail/1.5.4 To: CHEMISTRY!at!ccl.net MIME-Version: 1.0 Content-Type: Text/Plain; charset="iso-8859-1" Content-Description: clearsigned data Content-Disposition: inline Message-Id: <200403241611.44023.bernd.schubert!at!pci.uni-heidelberg.de> Sender: Bernd Schubert X-Spam-Status: No, hits=0.0 required=7.0 tests=none 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 i2OF8xjs002880 -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi all, I'm already trying to forward this mail from the Beowulf list for more than four weeks, maybe it works this time (it seems that my default smpt-provider is blocked) Cheers, Bernd - ---------- Forwarded Message ---------- Subject: [Beowulf] 64-bit Gaussian 03 on Opteron/SuSE Date: Sunday 22 February 2004 10:32 From: Jyh-Shyong Ho To: beowulf!at!beowulf.org Cc: ccwu!at!mail.nchu.edu.tw Hi, We have managed to built a native 64-bit version of Gaussian 03 Rev.B05 on a dual Opteron box running SLSE8 for AMD64 with 64-bit PGI Workstation 5.1.3 compiler and 64-bit GOTO library. We ran all the test cases included in Gaussian 03 source code and compared the results against the reference results ran on SGI. All tests cases are successfully completed except test602 and test605 with error at the last stage when l9999 tries to close files. There are several files in directory bsd need some modification: machine.c (add one section to return "x86_64" as machine identification) mdutil.c (add one section for x86_64) mdutil.f (add one section for x86_64) bldg03 (modify the file so it can pick up x86_64.make as g03.make) and create a make file x86_64.make (use i386.make as a template) The compiler used is pgf90, but l906 and l609 has to be compiled with pgf77, in order to pass all the test cases. We are running more tests and comparing the performance of 64-bit version abd 32-bit version. Regards Jyh-Shyong Ho, Ph.D. Research Scientist National Center for High-Performance Computing Hsinchu, Taiwan, ROC _______________________________________________ Beowulf mailing list, Beowulf!at!beowulf.org To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf - ------------------------------------------------------- - ------------------------------------------------------- - ------------------------------------------------------- - -- Bernd Schubert Physikalisch Chemisches Institut / Theoretische Chemie Universitdt Heidelberg INF 229 69120 Heidelberg e-mail: bernd.schubert!at!pci.uni-heidelberg.de -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.4 (GNU/Linux) iD8DBQFAYaUqLR5WR6DFumYRAuS2AKC39ohfsOp2c5By9Y3YlNrXbczqkACfWf4R szcY3ZMDIpsfQnDOLm36xjc= =Agrs -----END PGP SIGNATURE----- From chemistry-request@ccl.net Wed Mar 24 13:53:18 2004 Received: from MM01SNLNTO.son.sandia.gov (mm01snlnto.sandia.gov [132.175.109.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2OIrGjs008946 for >ccl.net>; Wed, 24 Mar 2004 13:53:16 -0500 Received: from 132.175.109.1 by MM01SNLNTO.son.sandia.gov with ESMTP ( Tumbleweed MMS SMTP Relay 01 (MMS v5.6.1)); Wed, 24 Mar 2004 11:56:05 -0700 X-Server-Uuid: C223CCCD-D7BD-4D0E-A874-9ACF7D7E7905 Received: from sandia.gov (s848769.sandia.gov [134.253.246.160]) by sass165.sandia.gov (8.12.10/8.12.10) with ESMTP id i2OIu474000227 for >ccl.net>; Wed, 24 Mar 2004 11:56:05 -0700 (MST) Date: Wed, 24 Mar 2004 11:56:15 -0700 MIME-Version: 1.0 Subject: Orbital plotting references From: "Rick Muller" >sandia.gov> To: chemistry<>ccl.net Message-ID: >sandia.gov> X-Mailer: Apple Mail (2.553) X-PMX-Version: 4.5.0.90627, Antispam-Core: 4.0.4.92622, Antispam-Data: 2004.3.23.95127 X-WSS-ID: 6C7F064F124770473-01-01 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I'm interested in references to orbital plotting, that is, isosurfacing algorithms for 3D rendering of the results of quantum chemistry calculations. Most of these algorithms use Marching Cubes to draw the isosurfaces, and I'm particularly interested in adaptive schemes that people have come up with to do this quickly. I'll post a summary of responses I get... Rick Muller rmuller<>sandia.gov