From chemistry-request@www.ccl.net Tue Oct 20 06:37:55 1998 Received: from chemistry.leeds.ac.uk (chmsun1.leeds.ac.uk [129.11.12.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA24614 Tue, 20 Oct 1998 06:37:53 -0400 (EDT) Received: from [129.11.12.138] (chmmac37.leeds.ac.uk [129.11.12.138]) by chemistry.leeds.ac.uk (8.8.8/8.8.8) with ESMTP id LAA09554 for ; Tue, 20 Oct 1998 11:37:51 +0100 (BST) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Sender: darrena@chem.leeds.ac.uk Message-Id: Date: Tue, 20 Oct 1998 11:31:53 +0100 To: chemistry@www.ccl.net From: Darren Andrews Subject: Compiling CADPAC on Linux using Portland Group compiler Dear all, Has anyone managed to successfully compile Cadpac6 on a linux machine using the Portland Group compiler? I would like to get hold of a working Makefile for either the standard compiler or the high performance auto-parallelising version. Cheers, Darren Andrews. PostGraduate Student, School of Chemistry, University of Leeds, Leeds. LS2 9JT. England. Darrena@chem.leeds.ac.uk Tel: 0113 233 6594. Fax: 0113 233 6565. From chemistry-request@www.ccl.net Tue Oct 20 09:53:14 1998 Received: from interlock.amoco.com (interlock.amoco.com [192.195.167.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id JAA25294 Tue, 20 Oct 1998 09:53:12 -0400 (EDT) Received: by interlock.amoco.com id IAA05213 (InterLock SMTP Gateway 3.0 for CHEMISTRY@www.ccl.net); Tue, 20 Oct 1998 08:53:09 -0500 Message-Id: <199810201353.IAA05213@interlock.amoco.com> Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-4); Tue, 20 Oct 1998 08:53:09 -0500 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-3); Tue, 20 Oct 1998 08:53:09 -0500 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-2); Tue, 20 Oct 1998 08:53:09 -0500 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-1); Tue, 20 Oct 1998 08:53:09 -0500 From: jtgolab@amoco.com (Joe Golab) Date: Tue, 20 Oct 1998 09:03:10 -0500 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: SUMMARY -- Mass Spectrum Software Cc: ryszard@moldyn.com, jtgolab@amoco.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCL Readers: The inquiry about Mass Spectrum software, received the following four responses. I also received some surface mail from ChemSW. _____________________________ Forward Header _________________________________ Subject: simulation of mass spectra Author: eduffy (eduffy@pfizer.com) at unix,mime Date: 10/15/98 8:39 AM Joe - Are you familiar with Johann Gasteiger's work in this area? If not, have a look at the following url: http://www2.ccc.uni-erlangen.de/research/index.html I don't know if this is precisely for what you're looking, but it's in the ballpark. - Erin -- Dr. Erin M. Duffy email: eduffy@pfizer.com Pfizer Inc phone: (860) 441-1708 Eastern Point Road fax: (860) 441-4734 Groton, CT 06340 ======================================================================= LEGAL NOTICE: Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this e-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this e-mail or any action taken (or not taken) in reliance on it is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately. ======================================================================== _____________________________ Forward Header _________________________________ Subject: mass spec Author: gilson (gilson@indigo14.carb.nist.gov) at unix,sh Date: 10/15/98 8:20 AM I am not sure whether this would meet your needs... but NIST maintains and distributes a massive database of actual mass spec data. This is distributed with something like 80% of mass spec instruments as an aid to identifying molecules. If you are interested, you should be able to get information at www.nist.gov. Let me know if you need help finding this information. Best regards, Mike Gilson ------------------------------------------------------------------------------ Michael K. Gilson, Ph.D., M.D. Phone: (301) 738-6217 Center for Advanced Research in Biotechnology Fax: (301) 738-6255 National Institute of Standards and Technology 9600 Gudelsky Drive http://indigo15.carb.nist.gov/carb/gilson.html Rockville, MD 20850-3479 e-mail: gilson@indigo14.carb.nist.gov ------------------------------------------------------------------------------ _____________________________ Forward Header _________________________________ Subject: Re: CCL:Mass Spectrum Program Author: Robert.Hoellering (Robert.Hoellering@ccc.chemie.uni-erlangen.de) at unix,sh Date: 10/16/98 4:28 AM Have al look at our web site at http://www2.ccc.uni-erlangen.de/research/mass_spectroscopy/index.html if our programs are, what you are searching for. We have a series of fragmentation and rearrangenet types, but the set is not complete. Greatings, Robert Hoellering ---------------------------------------------------------------------------- | | | Dr. Robert Hoellering | | Computer-Chemie-Centrum | | Institut fuer Organische Chemie | | Universitaet Erlangen-Nuernberg | | Naegelsbachstrasse 25 | | 91052 Erlangen | | Germany | | | | Phone: +49/(0)9131/85-26574 | | FAX: +49/(0)9131/85-26566 | | Email: hoellering@ccc.chemie.uni-erlangen.de | | WWW: http://www2.ccc.uni-erlangen.de/people/Robert_Hoellering | | | ---------------------------------------------------------------------------- _____________________________ Forward Header _________________________________ Subject: Mass Spec analysis program Author: graham.smith (graham_smith@merck.com) at unix,mime Date: 10/16/98 6:29 AM Joe, There is a commercial program which will allow you to draw a structure and ask for either a one or two bond fragmentation pattern and it will then generate all of the fragments from the drawing. It is produced by WindowChem, I think. It is also about $300 or so depending on which version you get. We use it in my lab and find it quite helpful. The web site is: http://www.chemsw.com Hope this helps. Graham Smith graham_smith@merck.com >-- END -- :Joe jtgolab@amoco.com (630) 961-7878 +---------------------------------------------------------+ | Graffiti scrawled on a hand drier in a public restroom: | | "Push button for a message from your congressman." | +---------------------------------------------------------+ From chemistry-request@www.ccl.net Mon Oct 19 01:33:55 1998 Received: from imc01.ex.nus.edu.sg (imc01.ex.nus.edu.sg [137.132.14.60]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id BAA08650 Mon, 19 Oct 1998 01:33:54 -0400 (EDT) Received: by imc01.ex.nus.edu.sg with Internet Mail Service (5.5.2120.0) id ; Mon, 19 Oct 1998 13:35:13 +0800 Message-ID: <4B0D7BF452B9D011899D0020AFFBEE6101B821CD@exs03.ex.nus.edu.sg> From: Novak Igor To: "'chemistry@www.ccl.net'" Subject: dipole and magnetic moments for ions Date: Mon, 19 Oct 1998 13:35:12 +0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2120.0) Content-Type: text/plain Dear Netters, I have a question concerning molecular ions (singly, positively charged). I would appreciate if someone can point out the references where I can get info on how to obtain dipole and magnetic moments for such ions. I remember reading that dipole moment is not uniquely defined in such an ion, but I need to know more. Also, does anyone know references concerning MW studies of such ions? Many thanks! Dr I.Novak, Dept.of Chemistry, National University of Singapore, Singapore 119260 chmigorn@nus.edu.sg From chemistry-request@www.ccl.net Mon Oct 19 01:33:55 1998 Received: from imc01.ex.nus.edu.sg (imc01.ex.nus.edu.sg [137.132.14.60]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id BAA08650 Mon, 19 Oct 1998 01:33:54 -0400 (EDT) Received: by imc01.ex.nus.edu.sg with Internet Mail Service (5.5.2120.0) id ; Mon, 19 Oct 1998 13:35:13 +0800 Message-ID: <4B0D7BF452B9D011899D0020AFFBEE6101B821CD@exs03.ex.nus.edu.sg> From: Novak Igor To: "'chemistry@www.ccl.net'" Subject: dipole and magnetic moments for ions Date: Mon, 19 Oct 1998 13:35:12 +0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2120.0) Content-Type: text/plain Status: RO Content-Length: 524 Dear Netters, I have a question concerning molecular ions (singly, positively charged). I would appreciate if someone can point out the references where I can get info on how to obtain dipole and magnetic moments for such ions. I remember reading that dipole moment is not uniquely defined in such an ion, but I need to know more. Also, does anyone know references concerning MW studies of such ions? Many thanks! Dr I.Novak, Dept.of Chemistry, National University of Singapore, Singapore 119260 chmigorn@nus.edu.sg From chemistry-request@www.ccl.net Mon Oct 19 04:39:29 1998 Received: from zape.aula.eis.uva.es (zape.aula.eis.uva.es [157.88.141.253]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA08319 Mon, 19 Oct 1998 04:39:23 -0400 (EDT) Received: from localhost (rnunez@localhost) by zape.aula.eis.uva.es (8.9.1/8.9.1) with SMTP id JAA12210 for ; Mon, 19 Oct 1998 09:37:38 +0100 (MET) Date: Mon, 19 Oct 1998 09:37:38 +0100 (MET) From: Ricardo Nunez To: chemistry@www.ccl.net Subject: CCL: specific optical rotation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I need the experimental specific optical rotation values of a set of molecules: trans-1,2-dimethylcyclohexane trans-1,3-dimethylcyclohexane and other dimethyl, trimethyl, tetramethyl, ethyl-methy, diehtyl, etc cyclohexane derivatives. I would appreciate it if any one could give me some references to such experimental values. Thanks. Ricardo Nunez rnunez@dali.eis.uva.es From chemistry-request@www.ccl.net Mon Oct 19 04:39:29 1998 Received: from zape.aula.eis.uva.es (zape.aula.eis.uva.es [157.88.141.253]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA08319 Mon, 19 Oct 1998 04:39:23 -0400 (EDT) Received: from localhost (rnunez@localhost) by zape.aula.eis.uva.es (8.9.1/8.9.1) with SMTP id JAA12210 for ; Mon, 19 Oct 1998 09:37:38 +0100 (MET) Date: Mon, 19 Oct 1998 09:37:38 +0100 (MET) From: Ricardo Nunez To: chemistry@www.ccl.net Subject: CCL: specific optical rotation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: RO Content-Length: 415 Hello, I need the experimental specific optical rotation values of a set of molecules: trans-1,2-dimethylcyclohexane trans-1,3-dimethylcyclohexane and other dimethyl, trimethyl, tetramethyl, ethyl-methy, diehtyl, etc cyclohexane derivatives. I would appreciate it if any one could give me some references to such experimental values. Thanks. Ricardo Nunez rnunez@dali.eis.uva.es From chemistry-request@www.ccl.net Mon Oct 19 21:31:00 1998 Received: from risky3.thchem.siu.edu (risky3.thchem.siu.edu [131.230.89.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id VAA27520 Mon, 19 Oct 1998 21:30:59 -0400 (EDT) Received: from localhost (tapas@localhost) by risky3.thchem.siu.edu (AIX4.2/UCB 8.7/8.7) with SMTP id UAA05408 for ; Mon, 19 Oct 1998 20:34:51 -0500 (CDT) Date: Mon, 19 Oct 1998 20:34:51 -0500 (CDT) From: Tapas Kar To: "Comp. Chem. List" Subject: Summary: Risc/Silicon Graphics/multiprocessor PC/Digital ... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > Hi Everybody, > We are planning to buy a box who shall be fully dedicated for > Gaussian94/98 > jobs and can handle(in good manner) large molecules(50-100atoms) with say > 300+ basis sets. How fast are the multiprocessor PC with Linux compared to > others say Risc/Silicon Graphics/Digital Alpha/ or other(???)? > > Budget is within 30-35K. > REPLIES: In a nutshell: Speed-wise, the fastest Pentium II systems are on par, if not faster, than (many of ) the SGI, IBM, DEC workstations/servers. On a bang-per-buck basis, that places the commodity-type machines WAY ahead of the latter computers. Of course, then there are the Alpha based clones (to be had for <$3,000), which are much faster again... but compilation of G9x for Alpha/Linux is not trivial, as this platform is not (yet) supported by Gaussian, Inc., as far as I know. You may be interested in our G94 benchmark paper that just came out: "Computational Chemistry on Commodity-Type Computers", Nicklaus, M.C. et al., J. Chem. Inf. Comput. Sci. 38(5), 893-905 (1998). I can send you a reprint if you want; please let me know. If you have a subscription to JCICS, you can also get it of the ACS Web site, at http://pubs.acs.org/journals/jcisd8/index.html. Hope this helped. Regards, Marc ------------------------------------------------------------------------ Marc C. Nicklaus National Institutes of Health E-mail: mn1@helix.nih.gov Bldg 37, Rm 5B29 Phone: (301) 402-3111 37 Convent Dr, MSC 4255 Fax: (301) 496-5839 BETHESDA, MD 20892-4255 USA http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm Laboratory of Medicinal Chemistry, National Cancer Institute ------------------------------------------------------------------------ ******************* Before you invest all the money in new hardware, consider a performance gain you could also see from new software. Not Gaussian, but Jaguar (www.schrodinger.com). Particularly for systems as large as you describe. Jaguar doesn't have as many features as Gaussian but it generally runs faster (sometimes much faster) for singlepoint energies and geometry optimizations, especially for systems that large. Other types of calculations are also faster, due to the methodologies unique to Jaguar which speed up the evaluation of 2- electron integrals. You might be able to demo it to see if there is a significant advantage for your own needs. Bryan Marten, PhD bryan.marten@spcorp.com ******************** Hi! Maybe this site can help you: http://www.cmm.ki.si/parallel/summary.html Regards... ------------------------------)(-------------------------- Jose Luis Carreon Macedo Quimica y Fisica Teorica,DEPg, Facultad de Quimica,UNAM,CU Mexico,DF. 04510 email: joseluis@eros.pquim.unam.mx -------------------------------------------- Tapas Kar, Ph. D Asst. Scientist/Asst. Professor (Adjunct) Forestry Bldg 118 Department of Chemistry Southern Illinois University at Carbondale Illinois 62901-4409 Fax: (618) 453 6408 Tel: (618) 453 6433(Lab) 6485(Office) -------------------------------------------- From chemistry-request@www.ccl.net Tue Oct 20 12:08:58 1998 Received: from mnvax.irfmn.mnegri.it (mnvax.irfmn.mnegri.it [195.61.203.11]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id MAA18226 Tue, 20 Oct 1998 12:08:57 -0400 (EDT) Received: from [195.61.203.156] by 195.61.203.156 with SMTP; Tue, 20 Oct 1998 18:08:20 +0200 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 20 Oct 1998 18:08:53 +0200 To: chemistry@www.ccl.net From: Benfenati Emilio Subject: Symposium on Predictive Toxicology of Chemicals Dear colleague, this is to announce the Symposium: PREDICTIVE TOXICOLOGY OF CHEMICALS: EXPERIENCES AND IMPACT OF ARTIFICIAL INTELLIGENCE TOOLS Stanford University (CA), March 22-24, 1999 within the American Association for Artificial Intelligence Spring Symposium Series" to which I sincerely hope you will feel inclined to reply. The call is available at: http://www.elet.polimi.it/AAAI-PT or can be requested to me as a text file. Please note that THE DEADLINE IS OCTOBER 30. Yours sincerely, Emilio Benfenati *********************************************************** Dr Emilio Benfenati Head, Laboratory of Environmental Chemistry and Toxicology Istituto di Ricerche Farmacologiche "Mario Negri" Via Eritrea 62, 20157 Milano, Italy Tel: +39-2-39014420 Fax: +39-2-39001916 e-mail: benfenati@irfmn.mnegri.it http://www.irfmn.mnegri.it/ambsal/chem-toxi/Default.htm *********************************************************** From chemistry-request@www.ccl.net Tue Oct 20 20:25:42 1998 Received: from uxmail.ust.hk (root@uxmail.ust.hk [143.89.14.30]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id UAA15768 Tue, 20 Oct 1998 20:25:40 -0400 (EDT) Received: from chzm68.ust.hk ([143.89.55.138]:1166 "EHLO ust.hk" ident: "NO-IDENT-SERVICE") by uxmail.ust.hk with ESMTP id <626055-13750>; Wed, 21 Oct 1998 08:24:30 +0800 Message-ID: <362D9AE7.B3AC6C2C@ust.hk> Date: Wed, 21 Oct 1998 08:27:21 +0000 From: Zhenyang LIN Reply-To: chzlin@ust.hk Organization: Chemistry/HKUST X-Mailer: Mozilla 4.04 (Macintosh; I; 68K) MIME-Version: 1.0 To: "CHEMISTRY@www.ccl.net" Subject: Successful stories wanted Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Dear CCLers, As a computational chemist, I was really excited that the Nobel Prize in chemistry was awarded to computational/theoretical chemists this year. I have been invited to give a lecture to the public on what the impact is of computational chemistry. I'd be very grateful if you can direct me to some successful stories of computational chemistry related to drug design and material sciences. It is better that these stories are understandable to the general public. Thank you in advance. -- Zhenyang LIN Assistant Professor Chemistry Dept HKUST Fax no: (+852)23581594 email: chzlin@ust.hk http://home.ust.hk/~chzlin/