From chemistry-request@server.ccl.net Mon Oct 11 04:49:52 1999 Received: from tdsede-exg.tdsede.dom ([194.235.134.141]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA25917 for ; Mon, 11 Oct 1999 04:49:50 -0400 Received: by TDSEDE.EXG with Internet Mail Service (5.5.2232.9) id <4B5CQFST>; Mon, 11 Oct 1999 09:43:37 +0100 Message-ID: <314CB0E40556D2118D930000C07CAAF665B2@TDSEDE.EXG> From: Paulo Couto To: "'chemistry@www.ccl.net'" Subject: CCL: How to specify 6-311++G** basis set using gamess Date: Mon, 11 Oct 1999 09:43:33 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2232.9) Content-Type: text/plain; charset="iso-8859-1" Dear CClers, I am trying to use previously optimized geometries in g94 with HF method and 6-311++G** basis set as input to gamess calculations, namely morokuma analysis. The basis specified in gamess is as follows: $BASIS GBASIS=N311 NGAUSS=6 NDFUNC=1 NPFUNC=1 DIFFSP=.TRUE. DIFFS=.TRUE. POLAR=POPN311 $END That should be equivalent to the basis set used in gaussian94. In reality, I get: GAMESS: TOTAL NUMBER OF BASIS FUNCTIONS = 37 G94: 36 basis functions which obviously leads to different results. Is the basis set correctly specified in my gamess input? Is there any detail I am missing here? Thank you in advance. Cumprimentos Paulo Couto ( pauloc@tduarte.pt ) + ----------------------------------------------------------------------- + | Unix is user friendly, it simply chooses its friends wisely ! | + ----------------------------------------------------------------------- + From chemistry-request@server.ccl.net Mon Oct 11 05:23:57 1999 Received: from srvnt01.osmetech.plc.uk (aromascn.demon.co.uk [158.152.95.246]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA26072 for ; Mon, 11 Oct 1999 05:23:54 -0400 Received: by SRVNT01 with Internet Mail Service (5.0.1460.8) id <4P5G15HT>; Mon, 11 Oct 1999 10:19:55 +0100 Message-ID: <09433A5B7967D3119BE30090278D112301AEB4@SRVNT01> From: Tom Hawkins To: "'CHEMISTRY@ccl.net'" Subject: RE: Question About Structure/Viewing Software Date: Mon, 11 Oct 1999 10:19:54 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1460.8) Content-Type: text/plain Rolf Claessen [mailto:administration@claessen.net] wrote: > for > visualization I > would recommend the free program swissPDB in combination with > POV Ray (also > free and maybe the best raytracer). I find that WebLabViewer Lite (free from MSI, http://www.msi.com) also generates nice pictures of smaller molecules and is easy to use. HTH Dr Tom Hawkins Osmetech plc Sensor Technologist Electra House, Electra Way, Crewe CW1 6WZ thawkins@osmetech.plc.uk Tel +44(0)1270 216444 Fax +44(0)1270 216030 From chemistry-request@server.ccl.net Mon Oct 11 05:35:16 1999 Received: from srvnt01.osmetech.plc.uk (aromascn.demon.co.uk [158.152.95.246]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA26176 for ; Mon, 11 Oct 1999 05:35:15 -0400 Received: by SRVNT01 with Internet Mail Service (5.0.1460.8) id <4P5G15HZ>; Mon, 11 Oct 1999 10:31:27 +0100 Message-ID: <09433A5B7967D3119BE30090278D112301AEB5@SRVNT01> From: Tom Hawkins To: "'CCL list'" Subject: Looking for mol modelling/q chem course in UK Date: Mon, 11 Oct 1999 10:31:26 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1460.8) Content-Type: text/plain Hi all, I am looking for a short course in molecular modelling/quantum chemistry to be held in the UK sometime in the next few months, perhaps covering the theory and use of packages such as MOPAC. My specific interest is in calculating theoretical parameters of small molecules for QSAR-type studies, though not for drug design. I'd also be interested in anything on dynamic simulations and modelling of polymers. Thanks in advance for any suggestions, Dr Tom Hawkins Osmetech plc Sensor Technologist Electra House, Electra Way, Crewe CW1 6WZ thawkins@osmetech.plc.uk Tel +44(0)1270 216444 Fax +44(0)1270 216030 From chemistry-request@server.ccl.net Mon Oct 11 07:10:08 1999 Received: from mail-c.bcc.ac.uk (mail-c.bcc.ac.uk [144.82.100.23]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA27409 for ; Mon, 11 Oct 1999 07:10:08 -0400 Received: from socrates-a.ucl.ac.uk by mail-c.bcc.ac.uk with SMTP (Mailer); Mon, 11 Oct 1999 12:04:57 +0100 From: uccatvm Message-Id: <9608.199910111104@socrates-a.ucl.ac.uk> Subject: Re: How to specify 6-311++G** basis set using gamess To: chemistry@server.ccl.net (CCL) Date: Mon, 11 Oct 1999 12:04:58 +0100 (BST) Cc: T.vanMourik@UCL.ac.uk (Tanja van Mourik) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi Paulo, > I am trying to use previously optimized geometries in g94 with HF method and > 6-311++G** basis set > as input to gamess calculations, namely morokuma analysis. > The basis specified in gamess is as follows: > > $BASIS GBASIS=N311 NGAUSS=6 NDFUNC=1 NPFUNC=1 DIFFSP=.TRUE. DIFFS=.TRUE. > POLAR=POPN311 $END > > That should be equivalent to the basis set used in gaussian94. In reality, I > get: > > GAMESS: TOTAL NUMBER OF BASIS FUNCTIONS = 37 > > G94: 36 basis functions > I assume the difference is caused by GAMESS using cartesian instead of spherical harmonic basis functions (i.e., 6 instead of 5 d functions). AFAIK, GAMESS version 6.2 allows the use of sperical harmonic basis functions, but I think previous versions don't. hope that helps, Tanja -- ==================================================================== Tanja van Mourik phone University College London work: +44 (0)171-504-4665 Christopher Ingold Laboratories home: +44 (0)1895-259-312 20 Gordon Street e-mail London WC1H 0AJ work: T.vanMourik@ucl.ac.uk United Kingdom home: tanja@netcomuk.co.uk ==================================================================== From chemistry-request@server.ccl.net Mon Oct 11 11:02:26 1999 Received: from nmr.utmb.edu (dggin1.utmb.edu [129.109.73.3]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA28544 for ; Mon, 11 Oct 1999 11:02:25 -0400 Received: from nmr.utmb.edu (morass.utmb.edu [129.109.73.39]) by nmr.utmb.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id JAA11171; Mon, 11 Oct 1999 09:58:13 -0500 Sender: bruce@nmr.utmb.edu Message-ID: <3801FB44.7873B325@nmr.utmb.edu> Date: Mon, 11 Oct 1999 09:59:16 -0500 From: "Bruce A. Luxon" Reply-To: bruce@nmr.utmb.edu Organization: Sealy Center for Structural Biology X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net CC: tjm@spawn.scs.uiuc.edu Subject: Summary: SGI Sleds Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I received the following very helpful posts regarding where to get sleds for SGI's. Thanks to all. Bruce -=-=-==-=-=-=-=-= From: Istvan Enyedy I think it's better if you use external devices. In this case if you decide to switch to Octane or O2 you can move all your external devices to the new computer. Note to Istvan: I'm taking several Indigos out of service and want to put the various drives in some Indigo2s. Sleds are not interchangeable between Indigos and Indigo2s. -=-=-=-=-=-=-=-=-= From: Gregory Durst Here's a site that tells you everything you ever wanted to know (and more) about SGI drive sleds... http://www.amazing.com/internet/sgi-sleds.html For hardware try these places ... http://www.pacexp.com/sgisleds.htm and http://www.reputable.com/ -=-=-=-=-=-=-=-=- From: Bienstock.Rachelle I would try to contact some of the third party vendors of SGI equipment: Try Western Scientific (http://www.wsm.com/) SGI uses their own design of sleds, and so they are quite pricey compared to PC sleds. ($300 is a bit much....they should be on the order of $75- $200). The best deal is to buy the disks with the SGI sleds. Western Scientific will sell you disks already attached to SGI sleds for very competitive prices (i.e. much less than SGI itself). P.S. I don't work for Western Scientific, but I have purchased numerous disks and tape systems from them for my SGIs. -=-=-=-=-=-=-=- From: David Reichert Check with Boost PERIPHERAL Systems (www.boostsystems.com) sleds for a bare harddrive for my indigo2 ran less than $100 as I recall. That was with the drive. dave reichert =-=-=-=-=-=-=-=-=- From: Steven K. Pollack Try Impediment: Impediment, Inc. 541 Plain St. Marshfield, MA 02050 (781) 834-3800 -=-=-=-=-=-=- From: Jen Sorensen I'm not sure about their stock for Indigo2's, but I have had only positive experiences with Zzyzx Peripherals. Reasonable prices and good service. (www.zzyzx.com -or- 1-800-876-7818) -- =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Bruce A. Luxon, Ph.D. Associate Professor Sealy Center for Structural Biology Dept. of Human Biological Chemistry & Genetics University of Texas Medical Branch Galveston, TX 77555-1157 (409)747-6802; Fax (409)747-6850 http://www.hbcg.utmb.edu/ http://www.nmr.utmb.edu/ mailto:bruce@nmr.utmb.edu =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Mon Oct 11 13:46:21 1999 Received: from trifid.u.arizona.edu (root@trifid.U.Arizona.EDU [128.196.137.197]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA29123 for ; Mon, 11 Oct 1999 13:46:21 -0400 Received: from u.arizona.edu (kinghorn@lapc3.chem.Arizona.EDU [128.196.184.166]) by trifid.u.arizona.edu (8.8.8/8.8.8) with ESMTP id KAA30212; Mon, 11 Oct 1999 10:41:14 -0700 Sender: kinghorn@u.arizona.edu Message-ID: <3802213A.3D9D85EC@u.arizona.edu> Date: Mon, 11 Oct 1999 10:41:14 -0700 From: "Donald B. Kinghorn" Organization: University of Arizona X-Mailer: Mozilla 4.61 [en] (X11; I; Linux 2.2.13-7mdk i686) X-Accept-Language: en MIME-Version: 1.0 To: beowulf@beowulf.org, chemistry@ccl.net Subject: Beowulf+Chemistry web site Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all, Sorry I've been over a week getting back to this ... I gave my talk and it went very well ... looks like there will be two more beowulf projects in the department in addition to what our group is doing. Success! :-) [the only bad(?) part is that the other projects actually have money to work with and we don't -- Oh well.] I have managed to get 4 dual PII400 boxes together that I can use for a dedicated beowulf. I'll be setting it up this week. I made some web pages for the talk. The site is definitely "under construction". I'll try to work on the site since there seems to be some interest. The theme is "Beowulf Clusters for Chemists". http://www.chem.arizona.edu/theochem/beowulf The promised summary of e-mail responses to my original posting is at http://www.chem.arizona.edu/theochem/beowulf/chemsites.html Again, thanks for the replies. I had hoped to get some more work done on the site before I announced but it may be another week before I get back to it, so... Best wishes -Don +++++++++++++++++++++++++++++++++++++++++++ Dr. Donald B. Kinghorn Theoretical and Computational Chemistry Group University of Arizona Dept. of Chemistry Tucson AZ kinghorn@u.arizona.edu +++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Mon Oct 11 11:44:35 1999 Received: from mtiwmhc03.worldnet.att.net (mtiwmhc03.worldnet.att.net [204.127.131.38]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA28724 for ; Mon, 11 Oct 1999 11:44:35 -0400 Received: from dell ([63.21.232.242]) by mtiwmhc03.worldnet.att.net (InterMail v03.02.07.07 118-134) with SMTP id <19991011153924.DLNO20426@dell>; Mon, 11 Oct 1999 15:39:24 +0000 Message-Id: <3.0.6.32.19991011083832.007e38b0@postoffice.worldnet.att.net> X-Sender: davidgallagher@postoffice.worldnet.att.net X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Mon, 11 Oct 1999 08:38:32 -0700 To: Tom Hawkins From: David Gallagher Subject: Looking for mol modelling/q chem course in UK Cc: CHEMISTRY@ccl.net In-Reply-To: <09433A5B7967D3119BE30090278D112301AEB5@SRVNT01> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi Tom, At 10:31 AM 10/11/99 +0100, Tom Hawkins wrote: >Hi all, > >I am looking for a short course in molecular modelling/quantum chemistry to >be held in the UK sometime in the next few months, perhaps covering the >theory and use of packages such as MOPAC. My specific interest is in >calculating theoretical parameters of small molecules for QSAR-type studies, >though not for drug design. I'd also be interested in anything on dynamic >simulations and modelling of polymers. > >Thanks in advance for any suggestions, > >Dr Tom Hawkins Osmetech plc >Sensor Technologist Electra House, Electra Way, Crewe CW1 6WZ >thawkins@osmetech.plc.uk Tel +44(0)1270 216444 Fax +44(0)1270 216030 Fujitsu FQS (contact Jerzy M Rudzinski ) is sponsoring a series of seminars covering applications of MOPAC (including QSAR & QSPR with MOPAC) throughout Europe later this month. Jimmy Stewart (author of MOPAC) will be one of the speakers. Unfortunately, the only seminar set up for England will be at the University of Kent at Canterbury on Monday afternoon 18th October (contact Dr Simon Holder ). However, this seminar will focus mainly on QSAR and QSPR applications of MOPAC and on some reaction modelling with MOPAC. If you are unable to attend, I could email the stuff on QSAR (large Powerpoint file or just the references). Although, not part of this seminar, I also have some examples of predicting polymer properties (e.g. miscibilities, thermal degradation) with MOPAC. Let me know if I can help in any way. David Gallagher Fujitsu From chemistry-request@server.ccl.net Mon Oct 11 14:37:11 1999 Received: from motgate.mot.com (motgate.mot.com [129.188.136.100]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA29575 for ; Mon, 11 Oct 1999 14:37:10 -0400 Received: [from pobox2.mot.com (pobox2.mot.com [136.182.15.8]) by motgate.mot.com (MOT-motgate 1.0) with ESMTP id NAA05713 for ; Mon, 11 Oct 1999 13:32:21 -0500 (CDT)] Received: [from emailchd.sps.mot.com (emailchd.sps.mot.com [216.7.10.16]) by pobox2.mot.com (MOT-pobox2 2.0) with ESMTP id NAA02393 for ; Mon, 11 Oct 1999 13:32:20 -0500 (CDT)] Received: from email.mot.com (korkin@fritz [223.189.20.101]) by act.sps.mot.com (8.8.6 (PHNE_14041)/8.8.6) with ESMTP id LAA25905 for ; Mon, 11 Oct 1999 11:32:19 -0700 (MST) Sender: korkin@act.sps.mot.com Message-ID: <38022D32.BD325058@email.mot.com> Date: Mon, 11 Oct 1999 11:32:18 -0700 From: Anatoli Korkin X-Mailer: Mozilla 4.06 [en] (X11; I; HP-UX B.10.20 9000/782) MIME-Version: 1.0 To: CCL Subject: -OH...Cl Bond length? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleagues, Sorry, for the very specific question. Can some one point on experimentally measured H-Bond distances for any -OH...Cl systems. If OH is bound to a transition metal, it is the best I need. Theoretical data are also welcome. I will cite in a paper, which will come out soon in JPC. You may increase your paper citation index :-) or just help me, if it not yours. Thanks, Anatoli -- ****************************************************************** Anatoli A. Korkin, Ph.D Computational Technology Laboratory Computational Chemist Semiconductor Products Sector Motorola Inc., MD M360 Tel: (480) 655-3171 2200 W. Broadway Road Fax: (480) 655-5013 Mesa AZ 85202 E.mail: r40757@email.mot.com ******************************************************************* From chemistry-request@server.ccl.net Mon Oct 11 17:17:46 1999 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA31140 for ; Mon, 11 Oct 1999 17:17:46 -0400 Received: (from daemon@localhost) by bioc1.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id OAA20969 for ; Mon, 11 Oct 1999 14:13:39 -0700 (PDT) Received: from jnauss-pc.msi.com(146.202.26.50) by bioc1.msi.com via smap (V2.0) id xmab20961; Mon, 11 Oct 99 14:13:33 -0700 Message-Id: <3.0.3.32.19991011134153.00804e20@146.202.6.217> X-Sender: jnauss@146.202.6.217 X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.3 (32) Date: Mon, 11 Oct 1999 13:41:53 -0700 To: CHEMISTRY@ccl.net From: "Jeffrey L. Nauss" Subject: MSI Workshops on Small Molecule/Drug Design and Combinatorial Chemistry Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Molecular Simulations Inc. will be holding a pair of workshops focusing on Cerius2 at the San Diego Supercomputer Center, La Jolla, CA. On November 15-16, the workshop "Small Molecule/Drug Design" will be held. This is an introductory course that focuses on the analysis of structure-activity relationships and receptor-pharmacophore interaction patterns with application to the drug discovery process. It uses the Cerius2 user interface and also introduces Catalyst. On November 17-18, the "Combinatorial Chemistry" workshop will be given. This workshop is an introduction to library design and analysis in combinatorial techniques. It also uses the Cerius2 interface. Attendees should possess knowledge of basic UNIX commands and have a basic understanding of QSAR theory. Both suggested prerequisites can be met by attending the Small Molecule/Drug Design workshop. Fees for each 2-day course are $1000 commercial, $500 government, and $400 academic. However, register for both courses and receive a 25% discount for the second workshop. Further detailed information about this and other MSI training workshops, as well as on-line course registration, can be found at MSI's website (http://www.msi.com/about/events/training). Please do not hesitate to contact me should you have any questions. Thank you very much. Jeffrey L. Nauss MSI Customer Training Programs (858) 799-5555 -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Customer Training Programs Fax: (858) 458-0136 Molecular Simulations Inc. E-mail: jnauss@msi.com 9685 Scranton Road http://www.msi.com/about/events/training San Diego, CA 92121