From chemistry-request@server.ccl.net Tue Sep 25 01:44:33 2001 Received: from office.nankai.edu.cn ([202.113.22.33]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8P5i0103350 for ; Tue, 25 Sep 2001 01:44:31 -0400 Received: from chemiprinter ([202.113.28.189]) by office.nankai.edu.cn (8.10.0.Beta6/8.10.0.Beta6) with SMTP id f8PJGbf03084 for ; Tue, 25 Sep 2001 14:16:43 -0500 Message-Id: <200109251916.f8PJGbf03084@office.nankai.edu.cn> Date: Tue, 25 Sep 2001 13:44:35 +0800 From: Ace Breakpoint Reply-To: bpint@eyou.com To: "chemistry@ccl.net" Subject: Request for Help: SGI/G98 problem X-mailer: FoxMail 3.1 beta [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Hi, everyone, I managed to install Gaussian 98 Rev. A5 on a SGI(IP27) workstation. It seemed that the process of compiling completed normally. But when I run a test job, the following exception occured(no matter what the test job was): hostname% g98 < test.com Entering Gaussian System, Link 0=g98 Initial command: /path/g98/l1.exe /tmp/Gau-106523.inp -scrdir=/tmp Entering Link 1 = /path/g98/l1.exe PID= 106528. ... ... ... *************************************** Gaussian 98: SGI-G98RevA.5 21-Sep-1998 26-Sep-2001 *************************************** Default route: MaxDisk=512MB ----------------------------------------------- #T B3LYP/6-31+G(d) SCRF(IPCM) SCF=Tight Test 6D ----------------------------------------------- ------------------------ TRANS-1,2-DICHLOROETHANE ------------------------ Symbolic Z-matrix: Floating Exception hostname% What does a "floating exception" mean? How can I get it run smoothly? Thank you very much for your advancing help! Ace Breakpoint From chemistry-request@server.ccl.net Tue Sep 25 00:11:26 2001 Received: from smtp.csc.fi ([193.166.0.99]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8P4BP113906 for ; Tue, 25 Sep 2001 00:11:26 -0400 Received: from ISOSIRRI (dhcp-28.csc.fi [193.166.2.28]) by smtp.csc.fi (8.9.3/8.9.3/CSC) with ESMTP id HAA05895; Tue, 25 Sep 2001 07:11:24 +0300 From: "Leif Laaksonen" To: "'Pornthep Sompornpisut'" , Subject: RE: Q:Molecular visualization software for Pocket PC Date: Tue, 25 Sep 2001 07:11:14 +0300 Message-ID: <000401c14578$1df4d060$1c02a6c1@ISOSIRRI> 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 10.0.2627 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal In-Reply-To: <3.0.6.32.20010924110702.00a7b4c0@unix.mail.virginia.edu> Hi, I remember seeing that HyperChem worked on Handheld PC but I don't know of any molecular modelling software for Pocket PC. However, you can write out your structures using VRML and use the VRML browser on your Pocket PC. I use this to take structures with me in my pocket. Regards, -leif laaksonen -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net] On Behalf Of Pornthep Sompornpisut Sent: Monday, September 24, 2001 6:07 PM To: chemistry@ccl.net Subject: CCL:Q:Molecular visualization software for Pocket PC Dear Colleage, Does anyone know if there is any molecular modeling software that can run on Pocket PC or Handheld PDA? Thep ======================================================================= Pornthep Sompornpisut, Ph.D Postdoctoral Fellow Molecular Physiology & Biological Physics Department School of Medicine University of Virginia Tel: 804-924-5473 Fax: 804-982-1616 Email:ps2t@virginia.edu ======================================================================= -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Tue Sep 25 09:49:41 2001 Received: from fcindy13.ncifcrf.gov ([129.43.6.40]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8PDne126984 for ; Tue, 25 Sep 2001 09:49:40 -0400 Received: from localhost (mab@localhost) by fcindy13.ncifcrf.gov (SGI-8.9.3/8.9.3) with ESMTP id JAA29201; Tue, 25 Sep 2001 09:48:53 -0400 (EDT) Date: Tue, 25 Sep 2001 09:48:53 -0400 From: Buyong Ma To: cc: Subject: Re: CCL:covalent bond lenghts In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII try: Structure data of polyatomic molecules, Kuchitsu, K. Ed. Springer_Verlag, Berlin, 1992. ================================================================= Buyong Ma, PhD Laboratory of Experimental and Computational Biology National Cancer Institute Frederick, MD 21702, USA Voice (301) 846-6540 E-mail mab@fcindy13.ncifcrf.gov ================================================================= On Mon, 24 Sep 2001 maria.brandl@pharma.novartis.com wrote: > Dear CCL - folks, > > does anybody know where to get comprehensive > tabulated information on standard geometries (bond > lengths, angles) of chemical groups ? > > Cheers, > > Maria > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Tue Sep 25 10:55:56 2001 Received: from marcos.networkcs.com ([137.66.16.1]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8PEtu129047 for ; Tue, 25 Sep 2001 10:55:56 -0400 Received: from us.msp.networkcs.com (us.networkcs.com [137.66.12.15]) by marcos.networkcs.com (8.9.3/8.9.3) with ESMTP id JAA60275 for ; Tue, 25 Sep 2001 09:55:56 -0500 (CDT) (envelope-from rbw@networkcs.com) Received: (from rbw@localhost) by us.msp.networkcs.com (8.9.2/8.9.2) id JAA63669 for chemistry@www.ccl.net; Tue, 25 Sep 2001 09:55:56 -0500 (CDT) (envelope-from rbw) Date: Tue, 25 Sep 2001 09:55:56 -0500 (CDT) From: Richard Walsh Message-Id: <200109251455.JAA63669@us.msp.networkcs.com> To: chemistry@server.ccl.net Subject: G98 A.9/A.10 on Red Hat 7.1 Cluster ... All, Building G98 on PIII cluster running Red Hat 7.1. I have access to only A.9 at the moment which has an i386.make file that is 18 months old. Would like to compile using latest PGI options and ia32 makefile rather than the old one. A few questions: 1. Can someone diff the new and old makes and send the differences to me? Have folks added the options for SSE(1,2)? What are the experiences? 2. Which BLAS library has proven to be the best to work with? Can I use the ATLAS library? 3. Does anyone have experience with the Intel compiler which has SSE optimization build in? 4. What is the trick to bump up the shared memory maximum (shmmax trick) again? I am running on dual Tyan 2500 with 4G of memory. Kernal is configured to 4G. Any other memory issues or gotchas (I hate gotchas)? 5. Has anyone put together a HowTo on G98 cluster installation and tuning? If not, I will and send it out to the group. Regards, rbw #--------------------------------------------------- # # Richard Walsh # Project Manager, Cluster Computing, Computational # Chemistry and Finance # netASPx, Inc. # 1200 Washington Ave. So. # Minneapolis, MN 55415 # VOX: 612-337-3467 # FAX: 612-337-3400 # EMAIL: rbw@networkcs.com, richard.walsh@netaspx.com # #--------------------------------------------------- # "What you can do, or dream you can, begin it; # Boldness has genius, power, and magic in it." # -Goethe #--------------------------------------------------- # "Without mystery, there can be no authority." # -Charles DeGaulle #--------------------------------------------------- # "Why waste time learning when ignornace is # instantaneous?" -Thomas Hobbes #--------------------------------------------------- From chemistry-request@server.ccl.net Tue Sep 25 11:00:05 2001 Received: from ccdc.cam.ac.uk ([131.111.113.44]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8PF04129175 for ; Tue, 25 Sep 2001 11:00:04 -0400 Received: from ccdc.cam.ac.uk (sun29.ccdc.cam.ac.uk [131.111.113.6]) by ccdc.cam.ac.uk (8.9.1/8.9.1) with ESMTP id QAA11362 for ; Tue, 25 Sep 2001 16:00:03 +0100 (BST) Sender: bruno@ccdc.cam.ac.uk Message-ID: <3BB09BF3.671D52C3@ccdc.cam.ac.uk> Date: Tue, 25 Sep 2001 16:00:03 +0100 From: Ian Bruno Organization: Cambridge Crystallographic Data Centre X-Mailer: Mozilla 4.77 [en] (X11; U; SunOS 5.6 sun4u) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Mercury 1.0 - Crystal Structure Visualisation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Free Software for Crystal Structure Visualisation ================================================= The Cambridge Crystallographic Data Centre (CCDC) is pleased to announce the release of version 1.0 of its new crystal structure visualiser program Mercury. Mercury forms part of the Cambridge Structural Database (CSD) System, and will be shipped to subscribers in October 2001. However, we are also making Mercury available for anyone to download from the CCDC website, completely free of charge, as a service to the crystallographic and computational chemistry communities. Supported on Windows, Linux Intel, Solaris and SG IRIX operating systems, Mercury offers comprehensive facilities for visualising crystal structures in three dimensions, including: * full range of structure display styles, view directions, colours and structure manipulations * location and display of hydrogen bonding and other short contacts * ability to build and visualise a network of contacts * packing diagrams of single and multiple cell contents * measurement and display of geometrical parameters * display of centroids, least-squares mean planes and Miller planes * ability to generate and display slices through a crystal in any direction Additionally, Mercury offers; * downloading of hit lists from ConQuest [*] * browsing of the entire CSD or of in-house databases [*] * import of structures in other formats * the ability to save displays [*] only available if the CSD System is already installed We invite you to download Mercury from CCDC's website, use it, and feed back any comments that you have to us at: support@ccdc.cam.ac.uk Enhancement and development of Mercury will go on, guided by your feedback, and new updates will be made available for download. Please do tell others about Mercury - we'd like the program to be used as widely as possible. If you already subscribe to the CSD System, there is no need to wait until your October release arrives! You can find further details of Mercury, and links to download, at http://www.ccdc.cam.ac.uk/prods/mercury/ -- Dr Ian Bruno, CCDC, 12 Union Road, Cambridge, CB2 1EZ, UK Feedback and Support: support@ccdc.cam.ac.uk From chemistry-request@server.ccl.net Tue Sep 25 10:24:58 2001 Received: from mserv.rug.ac.be ([157.193.40.37]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8PEOw128495 for ; Tue, 25 Sep 2001 10:24:58 -0400 Received: from hartree4.rug.ac.be (hartree4.rug.ac.be [157.193.91.12]) by mserv.rug.ac.be (8.9.3/8.9.3) with ESMTP id QAA21844 for ; Tue, 25 Sep 2001 16:24:44 +0200 (MET DST) Received: (from tom@localhost) by hartree4.rug.ac.be (AIX4.2/UCB 8.7/8.7) id QAA08338; Tue, 25 Sep 2001 16:26:40 +0100 (NFT) Date: Tue, 25 Sep 2001 16:26:39 +0100 (NFT) From: Tom Kuppens To: chemistry@ccl.net Subject: Integration grid reference Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, i'm looking for some literature on the IR intensity accuracy with different integration grids in DFT calculations. Is there anyone who has got a reference on this subject? Thank you in advance, Tom Kuppens Ghent University tom@hartree4.ac.be http://studwww.rug.ac.be/~tkuppens/quantum/ --- It seems to me, Golan, that the advance of civilization is nothing but an exercise in the limiting of privacy. -- Janov Pelorat in Asimov's Foundation's Edge From chemistry-request@server.ccl.net Tue Sep 25 11:26:05 2001 Received: from data-csec.uk.informa.com ([213.212.68.130]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8PFQ1129618 for ; Tue, 25 Sep 2001 11:26:05 -0400 Received: from mort-ex1.uk.informa.com (unverified) by data-csec.uk.informa.com (Content Technologies SMTPRS 4.2.5) with ESMTP id for ; Tue, 25 Sep 2001 16:14:39 +0100 Received: by MORT-EX1 with Internet Mail Service (5.5.2653.19) id ; Tue, 25 Sep 2001 16:34:29 +0100 Message-ID: <24E82BA336E6D3118E420090275A75C008B95DA2@lonexch_srv.uk.informa.com> From: "Marshall, Chris" To: "'chemistry@ccl.net'" Subject: 02.02.13 Bioinformatics Event: InfotechPharma 2002, London, UK Date: Tue, 25 Sep 2001 16:24:21 +0100 InfotechPharma 2002: World Informatics Congress for Biopharm R&D http://www.infotechpharma.com/index.html?src=3D209 Wednesday 13 - Thursday 15 February, 2002 InfotechPharma is the annual meeting place for R&D and production informaticians working in pharma. Discovery, preclinical, clinical and production professionals from users, vendors and academia gather from around the world to pick up new ideas and check the ideas they have. News, reviews, benchmarking and bleeding edge technology combine to make this event unique. The congress is also home to the fastest growing informatics trade show around with well over 60 stands due. Targeted breakout sessions for discovery, development and regulatory affairs. Option Technologies interactive audience questionnaire on the state of the industry. Leading industry speakers and case studies. Trade show packed with product launches, seminars, workshops and mystery keynote speaker. Networking events throughout the day, every day. Training, networking and poster sessions for junior members of the informatics community. Sessions include: * Business Strategy * In silico biology * Infrastructure * Regulatory * Virtual Screening * Architecture * e-Clinical * Alliances * Information Mgt. * Validation http://www.infotechpharma.com/index.html?src=3D209 From chemistry-request@server.ccl.net Tue Sep 25 15:33:35 2001 Received: from prserv.net ([32.97.166.31]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8PJXZ101413 for ; Tue, 25 Sep 2001 15:33:35 -0400 Received: from attglobal.net (slip-32-101-203-234.in.us.prserv.net[32.101.203.234]) by prserv.net (out1) with SMTP id <2001092519333320101armrse>; Tue, 25 Sep 2001 19:33:33 +0000 Message-ID: <3865E6E1.F19D7A2@attglobal.net> Date: Sun, 26 Dec 1999 03:58:57 -0600 From: jmmckel@attglobal.net Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.51 [en]C-CCK-MCD (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: Leif Laaksonen CC: "'Pornthep Sompornpisut'" , chemistry@ccl.net Subject: Re: CCL:Q:Molecular visualization software for Pocket PC References: <000401c14578$1df4d060$1c02a6c1@ISOSIRRI> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit If I'm on target here, at least certain parts of Hyperchem work on PDA's.. ACS/Chicago-2001. John McKelvey Leif Laaksonen wrote: > Hi, > > I remember seeing that HyperChem worked on Handheld PC but I don't > know of any molecular modelling software for Pocket PC. > However, you can write out your structures using VRML and use > the VRML browser on your Pocket PC. I use this to take structures > with me in my pocket. > > Regards, > > -leif laaksonen > > -----Original Message----- > From: Computational Chemistry List [mailto:chemistry-request@ccl.net] On > Behalf Of Pornthep Sompornpisut > Sent: Monday, September 24, 2001 6:07 PM > To: chemistry@ccl.net > Subject: CCL:Q:Molecular visualization software for Pocket PC > > Dear Colleage, > > Does anyone know if there is any molecular modeling software that can > run on > Pocket PC or Handheld PDA? > > Thep > ======================================================================= > Pornthep Sompornpisut, Ph.D > Postdoctoral Fellow > Molecular Physiology & Biological Physics Department > School of Medicine > University of Virginia > Tel: 804-924-5473 > Fax: 804-982-1616 > Email:ps2t@virginia.edu > ======================================================================= > > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: > gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net