From chemistry-request@ccl.net Thu Feb 17 11:10:55 2005 Received: from mailer1.psc.edu (mailer1.psc.edu [128.182.58.100]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1HGAs4b005416 for ; Thu, 17 Feb 2005 11:10:54 -0500 Received: from pscuxc.psc.edu (pscuxc.psc.edu [128.182.66.177]) by mailer1.psc.edu (8.12.10/8.12.5) with ESMTP id j1HF3HbS011181 for ; Thu, 17 Feb 2005 10:03:17 -0500 (EST) Received: from pscuxc.psc.edu (localhost.psc.edu [127.0.0.1]) by pscuxc.psc.edu (8.12.10/8.12.5) with ESMTP id j1HF3GF0011043 for ; Thu, 17 Feb 2005 10:03:17 -0500 (EST) Received: from localhost (wymore@localhost) by pscuxc.psc.edu (8.12.10/8.12.8/Submit) with ESMTP id j1HF3GSA021654 for ; Thu, 17 Feb 2005 10:03:16 -0500 (EST) Date: Thu, 17 Feb 2005 10:03:15 -0500 (EST) From: Troy Wymore To: Subject: PSC Summer Workshop: Modeling Proteins and Nucleic Acids with AMBER, VMD and the MMTSB Toolkit In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: clamd / ClamAV version 0.75, clamav-milter version 0.75 on mailer1.psc.edu X-Virus-Status: Clean X-Spam-Status: No, hits=2.0 required=7.5 tests=IMPRONONCABLE_1, LINES_OF_YELLING autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net ********************************************* PSC BIOMEDICAL INITIATIVE WORKSHOP 2005 MODELING PROTEINS AND NUCLEIC ACIDS WITH AMBER, VMD AND THE MMTSB TOOLKIT June 9-12 Application Deadline: April 25 This workshop is funded by grants from the NIH National Center for Research Resources. These grants provide tuition, hotel, supercomputing time, and workshop materials for US academic participants. -------------------------- This workshop will cover the theory and practice of biomolecular simulations using the Amber suite of programs. The lectures will cover the use of molecular mechanics force fields, the theory of solvation effects, and the connections between simulations and thermodyanmic quantitites. Hands-on exercises will show how both implicit solvent and explicit solvent simulations can be carried out, visualized, and critically examined; participants are urged to bring specific projects > from their own labs to use as examples. More advanced topics will include treating part of the system (such as an enzyme active site) as a quantum region; using free energy simulations to estimate thermodynamic quantities; and using the MMTSB toolkit to accelerate sampling and to organize large-scale conformational explorations. Participants should have an understanding of physical chemistry at the undergraduate level, and be familiar with the basics of protein and/or nucleic acid struture and chemistry. Basic familiarity with the UNIX or Linux operating systems will be helpful. More information on the software to be used can be found at http://amber.scripps.edu (Amber), http://www.ks.uiuc.edu/Research/vmd (VMD), and http://mmtsb.scripp.edu (MMTSB) For specific details, including an electronic application form, see: www.psc.edu/biomed/training/workshops/2005/Amber/index.html If you have any questions, please contact Nancy Blankenstein at blankens !v! psc.edu From chemistry-request@ccl.net Thu Feb 17 19:22:40 2005 Received: from server.ccl.net (t157 [127.0.0.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1I0Md4b010534 for ; Thu, 17 Feb 2005 19:22:39 -0500 Received: (from apache@localhost) by server.ccl.net (8.12.8/8.12.8/Submit) id j1I0MdgH010532 for chemistry _(a)_ ccl.net; Thu, 17 Feb 2005 19:22:39 -0500 Date: Thu, 17 Feb 2005 19:22:39 -0500 Message-Id: <200502180022.j1I0MdgH010532 _(a)_ server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request _(a)_ ccl.net using -f From: "Jan, , Labanowski" To: chemistry _(a)_ ccl.net X-Web-Message-Number: 050217192214-10481 Subject: W:A major release of JUMBO system is available X-Spam-Status: No, hits=1.5 required=7.5 tests=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 Posting for: Peter Murray-Rust A major release of the JUMBO system (V4.6) is now available. It contains a substantial kit for processing XML+CML in chemistry, including much computational Chemistry, Java code, XSLT stylesheets, legacy converters and tools. Its primary language is Java 1.4, though there are tools for generating C++, Python and some F90/5 from the schema. The home page is on our Wiki at http://wwmm.ch.cam.ac.uk/moin/Jumbo4.6 and the initial jars will be posted during the next days. Adopters should be able to run Java 1.4. The working code has already been imported to the CML site at sourceforge (http://cml.sf.net) and can be checked out or browsed at http://cvs.sourceforge.net/viewcvs.py/cml/jumbo4.6/. There is now a substantial move towards XML as an infrastructure for computational chemistry, especially where programs need to be chained or where the throughput is high. CMLComp is capable of representing the input/output of compChem programs and interfaces have already been developed for codes such as GULP, GAMESS-US, MOPAC2003, SIESTA, and others. We are working with groups such as CCP-1, ABINIT, FSATOM, and the Open chemistry community. The distribution contains several papers describing the architecture and approach. We have already built an automatic system for high-throughput computing and tools for automatic conversion to XML of legacy program log files [both of these will be reported here shortly]. We are interested in hearing from anyone who would benefit from having an XMLised system. JUMBO is open source and interoperates with a number of other Open source efforts such as Jmol, Apache (Xindice, AXIS), Jchempaint/CDK, JOELib, OpenBabel, and ABINIT and we thank many collaborators P. Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069 From chemistry-request@ccl.net Thu Feb 17 15:31:59 2005 Received: from mailhub129.itcs.purdue.edu (mailhub129.itcs.purdue.edu [128.210.5.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1HKVv4b027402 for ; Thu, 17 Feb 2005 15:31:57 -0500 Received: from BPUTNAM3.itap.purdue.edu (bputnam3.rcs.purdue.edu [128.210.189.129]) (authenticated bits=0) by mailhub129.itcs.purdue.edu (8.13.1/8.13.1/avscan-smtp) with ESMTP id j1HKVurB004446 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for ; Thu, 17 Feb 2005 15:31:56 -0500 Date: Thu, 17 Feb 2005 15:31:57 -0500 (US Eastern Standard Time) From: Bryan Putnam To: CCL Subject: g03 on an IA32 platform running RH Enterprise Message-ID: X-X-Sender: bfp = mailhub016.itcs.purdue.edu MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-PMX-Version: 4.7.0.111621 X-PerlMx-Virus-Scanned: Yes X-Spam-Status: No, hits=0.0 required=7.5 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 all, I realize that Gaussian, Inc. officially supports only SuSE or Red Hat Linux on IA32 platforms. However, has anyone had any success in building an IA32 (i386, 32-bit) version of g03-C.02 (or any earlier version of g03) on a 32-bit system running Red Hat Enterprise? I was however able to get an IA64 (AMD64) version to work correctly on an Opteron64 running RHE. I was able to get an IA32 version of g03-C.02 to build and run correctly on a Debian system, but on a RH Enterprise system, we get the error message: Erroneous write during file extend. write -1 instead of 4096 Probably out of disk space. Write error in NtrExt1 I've tried lots of ideas, using pgi-5.1-4, pgi-5.1-6, pgi-5.2-4, tried linking statically, turned off optimization, etc., but no success Any ideas appreciated! Thanks, Bryan Bryan F. Putnam Rosen Center for Advanced Computing Information Technology at Purdue (ITaP) Young Hall 519 Ph 765-496-8225 Fax 765-494-0566 bfp = purdue.edu From chemistry-request@ccl.net Thu Feb 17 13:28:38 2005 Received: from ppsw-6.csi.cam.ac.uk (ppsw-6.csi.cam.ac.uk [131.111.8.136]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1HISb4b015646 for ; Thu, 17 Feb 2005 13:28:37 -0500 Received: from ursus.ch.cam.ac.uk ([131.111.121.19]:3381 helo=ursus.cam.ac.uk) by ppsw-6.csi.cam.ac.uk (smtp.hermes.cam.ac.uk [131.111.8.156]:25) with esmtp id 1D1pGQ-0001X8-Ky (Exim 4.44) (return-path ); Thu, 17 Feb 2005 17:16:32 +0000 Message-Id: <5.1.1.6.0.20050217165550.093b1420$at$pop.hermes.cam.ac.uk> X-Sender: pm286$at$pop.hermes.cam.ac.uk X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 Date: Thu, 17 Feb 2005 17:15:38 +0000 To: chemistry$at$server.ccl.net From: Peter Murray-Rust Subject: JUMBO and CML for compChem [ANNOUNCE] Cc: simon Tyrrell , yong Zhang In-Reply-To: <20050215054759.91793.qmail$at$web52303.mail.yahoo.com> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed 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=1.5 required=7.5 tests=FROM_ENDS_IN_NUMS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net A major release of the JUMBO system (V4.6) is now available. It contains a substantial kit for processing XML+CML in chemistry, including much computational Chemistry, Java code, XSLT stylesheets, legacy converters and tools. Its primary language is Java 1.4, though there are tools for generating C++, Python and some F90/5 from the schema. The home page is on our Wiki at http://wwmm.ch.cam.ac.uk/moin/Jumbo4.6 and the initial jars will be posted during the next days. Adopters should be able to run Java 1.4. The working code has already been imported to the CML site at sourceforge (http://cml.sf.net) and can be checked out or browsed at http://cvs.sourceforge.net/viewcvs.py/cml/jumbo4.6/. There is now a substantial move towards XML as an infrastructure for computational chemistry, especially where programs need to be chained or where the throughput is high. CMLComp is capable of representing the input/output of compChem programs and interfaces have already been developed for codes such as GULP, GAMESS-US, MOPAC2003, SIESTA, and others. We are working with groups such as CCP-1, ABINIT, FSATOM, and the Open chemistry community. The distribution contains several papers describing the architecture and approach. We have already built an automatic system for high-throughput computing and tools for automatic conversion to XML of legacy program log files [both of these will be reported here shortly]. We are interested in hearing from anyone who would benefit from having an XMLised system. JUMBO is open source and interoperates with a number of other Open source efforts such as Jmol, Apache (Xindice, AXIS), Jchempaint/CDK, JOELib, OpenBabel, and ABINIT and we thank many collaborators P. Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069