From toni@athe.wustl.edu Thu May 14 00:30:50 1998 Received: from athe.wustl.edu for toni@athe.wustl.edu by www.ccl.net (8.8.3/950822.1) id XAA06338; Wed, 13 May 1998 23:59:37 -0400 (EDT) Received: (from toni@localhost) by athe.wustl.edu (8.8.8/8.8.8) id WAA13986; Wed, 13 May 1998 22:57:57 -0500 (CDT) Date: Wed, 13 May 1998 22:57:57 -0500 (CDT) Message-Id: <199805140357.WAA13986@athe.wustl.edu> From: Toni Kazic To: arthur@csb0.IPC.PKU.EDU.CN CC: chemistry@www.ccl.net In-reply-to: (message from Arthur Wang on Thu, 14 May 1998 08:44:34 -0700 (PDT)) Subject: Re: CCL:Summary: Fuzzy logic Hi Arthur, one more reference: @book{negoita87, author = "Constantin Virgil Negoita and Dan Ralescu", title = "Simulation, Knoweldge-based Computing, and Fuzzy Statistics", publisher = "van Nostrand Reinhold", address = "New York", key = ai, year = 1987} I found this quite helpful. cheers, Toni Toni Kazic Institute for Biomedical Computing Washington University toni@athe.wustl.edu http://ibc.wustl.edu/~toni From h.rzepa@ic.ac.uk Tue May 12 11:30:33 1998 Received: from romeo.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.8.3/950822.1) id KAA25550; Tue, 12 May 1998 10:51:05 -0400 (EDT) Received: from oban.cc.ic.ac.uk [155.198.5.28] by romeo.ic.ac.uk with smtp (Exim 1.62 #1) id 0yZGNa-0001WQ-00; Tue, 12 May 1998 15:50:06 +0100 Received: from sg1.cc.ic.ac.uk ([155.198.63.8] helo=cscmgb.cc.ic.ac.uk) by oban.cc.ic.ac.uk with smtp (Exim 1.90 #1) for CHEMISTRY@www.ccl.net id 0yZGNa-0007np-00; Tue, 12 May 1998 15:50:06 +0100 Received: from [155.198.224.86] by cscmgb.cc.ic.ac.uk (940816.SGI.8.6.9/4.0) id PAA18083; Tue, 12 May 1998 15:50:05 +0100 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Sender: rzepa@155.198.63.8 Message-Id: Date: Tue, 12 May 1998 15:56:17 +0100 To: CHEMISTRY@www.ccl.net From: "Rzepa, Henry" Subject: ECHET98: Final call for abstracts Final Reminder: ECHET98: E-Conference on Heterocyclic chemistry A brief reminder that the deadline for abstract registration is this coming Friday. We have had a good response thus far, and are still aiming for the record number of submissions for ECHET96 (123). Almost everyone who has already registered has done so via http://www.ch.ic.ac.uk/ectoc/echet98/abs_reg.html so it cannot be that difficult! This gets you an article number and a password. Using this, you can "create" your article/poster by using http://www.ch.ic.ac.uk/cgi-bin/echet98/authors/abs_upload.sh or change any mistakes in the original registration using http://www.ch.ic.ac.uk/cgi-bin/echet98/authors/abs_updinfo.sh or add molecules to our database using http://www.ch.ic.ac.uk/ectoc/echet98/authors/mol_submit.html WHAT TO DO AFTER REGISTRATION You need to have your full poster/article in place by 19th June. You can do this by using the above methods to send us HTML style files, or if you are unfamiliar with this, send us a Word 6/97/98 document by email to mailto:echet98-submit@ic.ac.uk, remembering to tell us what your allocated article/poster number is. or by ftp to ftp://ftp.ch.ic.ac.uk (remember to use binary mode transfers). WHAT TO DO NOW Tell you colleagues etc to submit an abstract! Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; mailto:rzepa@ic.ac.uk; Tel (44) 171 594 5774; Fax: (44) 171 594 5804. URL: http://www.ch.ic.ac.uk/rzepa/ From d3e129@cagle.emsl.pnl.gov Tue May 12 13:30:33 1998 Received: from pnl.gov for d3e129@cagle.emsl.pnl.gov by www.ccl.net (8.8.3/950822.1) id NAA26786; Tue, 12 May 1998 13:14:21 -0400 (EDT) Received: from odyssey.emsl.pnl.gov by pnl.gov (PMDF V5.1-10 #21283) with ESMTP id <01IWXXRT0U5C8XMC7W@pnl.gov> for CHEMISTRY@www.ccl.net; Tue, 12 May 1998 10:14:18 PDT Received: from cagle.emsl.pnl.gov (cagle.emsl.pnl.gov [198.128.80.73]) by odyssey.emsl.pnl.gov (8.8.5/8.8.5) with ESMTP id KAA15754; Tue, 12 May 1998 10:14:17 -0700 (PDT) Received: (from d3e129@localhost) by cagle.emsl.pnl.gov (8.8.5/8.8.5) id KAA06833; Tue, 12 May 1998 10:14:18 -0700 (PDT) Date: Tue, 12 May 1998 10:14:18 -0700 (PDT) From: "Ricky A. Kendall" Subject: WCTCC 98 To: ricky.kendall@pnl.gov Reply-to: ra_kendall@pnl.gov Message-id: <199805121714.KAA06833@cagle.emsl.pnl.gov> Hello West Coast Theoretical Chemistry Conference (WCTCC) Colleagues, The WCTCC98 meeting will be at Pacific Northwest National Laboratory on June 21-23 (standard 2.5 day format, 1/2 day Sunday). Registration information and details are available at the following URL http://www.emsl.pnl.gov:2080/docs/wctcc98 Note: Don't forget the ":2080" or you will run into our firewall! Note: Also we have fixed many of the netscape 3.0 bugs!! :) DEADLINE for registration is May 22, 1998 (~10 days left!) Please register and submit your abstract on the Web at your earliest convenience. Also, please redistribute this information to all who might be interested in our meeting!! Thanks for your interest and we hope to see you in June. Student Stipends are available. Please see the stipend page off the WCTCC98 home page. Awards are made, based on the registration date! There is also a link on the web page to subscribe to the wctcc@emsl.pnl.gov mailing list (this message went to that list!). Regards, Ricky Kendall Rene Corrales Thom H. Dunning, Jr. David A. Dixon Michel Dupuis Administrative Coordinator: Sheri Perkins From lavelle@mbi.ucla.edu Wed May 13 00:30:39 1998 Received: from theta1.ben2.ucla.edu for lavelle@mbi.ucla.edu by www.ccl.net (8.8.3/950822.1) id XAA00369; Tue, 12 May 1998 23:59:51 -0400 (EDT) Received: from ewald.mbi.ucla.edu (ewald.mbi.ucla.edu [128.97.39.21]) by theta1.ben2.ucla.edu (8.8.8/8.8.8) with SMTP id UAA25700; Tue, 12 May 1998 20:59:45 -0700 Received: from red5.mbi.ucla.edu by ewald.mbi.ucla.edu (5.65v3.2/1.1.10.5/09Oct97-1217PM) id AA00215; Tue, 12 May 1998 20:59:45 -0700 Message-Id: <3.0.32.19980512210535.00ab84f0@mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Tue, 12 May 1998 21:05:36 -0700 To: hyperchem@hyper.com, chemistry@www.ccl.net, gamess-users@Glue.umd.edu From: Laurence Lavelle Subject: Large ab initio (scratch) files in HyperChem 5.1 Mime-Version: 1.0 Content-Type: text/enriched; charset="us-ascii" HyperChem 5.1 users and beta testers. Does HyperChem 5.1 detect NT and then support 64-bit file pointer semantics? i.e. What file size limitations have been noticed with HyperGauss in HC 5.1 Thanks Laurence
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Lab): (310) 206-8270 Phone (Office): (310) 825-2083 Fax: (310) 267-1957 http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" It will be a great day when schools have all the money they need, and the military has bake day sales. In nature's infinite book of secrecy A little I can read.
From tcg@chem.unipune.ernet.in Wed May 13 02:30:39 1998 Received: from naveen.ncst.ernet.in for tcg@chem.unipune.ernet.in by www.ccl.net (8.8.3/950822.1) id CAA00950; Wed, 13 May 1998 02:06:57 -0400 (EDT) Received: from unipune.ernet.in (unipune.ernet.in [196.1.114.1]) by naveen.ncst.ernet.in (8.6.12/8.6.6) with ESMTP id LAA07731 for ; Wed, 13 May 1998 11:46:05 +0530 Received: from chem.unipune.ernet.in by unipune.ernet.in (8.8.5/UNIPUNE-MAILHUB(02.04.97)) id LAA22855; Wed, 13 May 1998 11:28:20 -0500 (GMT) Received: by chem.unipune.ernet.in (8.7.5/SMI-SVR4) id LAA06126; Wed, 13 May 1998 11:42:35 -0500 Date: Wed, 13 May 1998 11:42:35 -0500 From: tcg@chem.unipune.ernet.in (Students of Dr. S.R. Gadre) Message-Id: <199805131642.LAA06126@chem.unipune.ernet.in> To: CHEMISTRY@www.ccl.net Subject: SO2--CO2 complexes Dear Sirs/Madams : I am interested in understanding the weak bonding in the complex between SO2 and CO2. I am aware only of thr work of Prof. R.L Kuczkowski on this topic. I would like to know about any recent works in this area. Thank you very much. Sicerely, Savita Pundlik From j.a.lumley@reading.ac.uk Wed May 13 12:30:45 1998 Received: from sumh1.rdg.ac.uk for j.a.lumley@reading.ac.uk by www.ccl.net (8.8.3/950822.1) id LAA03546; Wed, 13 May 1998 11:51:20 -0400 (EDT) Received: from indyq (actually host scsgind3) by sumh1.rdg.ac.uk; Wed, 13 May 1998 16:51:04 +0100 Received: from indyq by indyq via SMTP (940816.SGI.8.6.9/930416.SGI) for id QAA21629; Wed, 13 May 1998 16:51:03 +0100 Sender: james@reading.ac.uk Message-ID: <3559C166.794B@reading.ac.uk> Date: Wed, 13 May 1998 16:51:02 +0100 From: "James A.Lumley" X-Mailer: Mozilla 3.01Gold (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: CCL: G94 FOpt crash. Content-Type: multipart/mixed; boundary="------------15FB59E21CFB" --------------15FB59E21CFB Content-Type: text/plain; charset="us-ascii" Hi. I am running a series of single point G94 calculations using the 6-31G* basis set. One compound only requires extra ECP and radii to be defined in the input file (contains iodine) and this calculation runs fine. However, when i run a Geometry optimisation calculation to check my ECP are working fine, just adding FOpt into the input file, it will no longer run. The error given is that the radii is not specified. Below is a simple script for diatomic iodine which will run if you remove the FOpt keyword, but crashes if it is included. Any ideas what causes this? Input file attached below. Thanks -- James ************************************************************** mailto:J.A.Lumley@reading.ac.uk Chem Dept, Uni of Reading, Whiteknights RG6 6AD UK Ph: (0118) 9875123 ext.7415 ************************************************************** --------------15FB59E21CFB Content-Disposition: inline; filename="molec_iodine.com" Content-Type: text/plain; charset="us-ascii"; name="molec_iodine.com" $ RunGauss %Chk=molec_iodine.chk # HF/6-31G* FOpt ExtraBasis # Pop=(Reg,ChelpG,ReadRadii) # SCF=Direct Geom=(NoDistance,NoAngle) Gaussian generated by Cerius2 0 1 I I 1 r2 r2 2.764000 I 0 S 4 1.0 42297.957 0.0165457 6375.1354 0.1164656 1447.6218 0.4309597 390.94964 0.5667813 S 3 1.0 582.20124 -0.1144000 67.838092 0.6457644 29.640666 0.4265016 S 3 1.0 54.589064 -0.2773274 10.070202 0.8671635 4.5676679 0.2890370 S 3 1.0 8.8441340 0.3569170 2.0968138 -0.8254301 0.98611692 -0.3901444 S 2 1.0 1.5207770 0.2698431 0.27302449 -0.7625119 S 1 1.0 0.10795603 1.0000000 P 4 1.0 1997.5692 0.0239358 470.17426 0.1641003 147.12001 0.4915455 51.632190 0.4795349 P 3 1.0 158.66544 -0.0253934 21.085556 0.4791351 8.3903226 0.5879478 P 3 1.0 3.5785818 0.4341764 1.6034530 0.5290721 0.70343694 0.1113815 P 2 1.0 0.41515416 -0.3908686 0.17098833 -0.5190582 P 1 1.0 0.06856211 1.0000000 D 4 1.0 238.44881 0.0382347 69.545921 0.2205252 24.677895 0.5210939 9.0881485 0.4279063 D 3 1.0 5.9337495 0.2777183 2.2186322 0.5733560 0.80937642 0.3207317 D 1 1.0 0.266 1.000 **** 53 2.00 --------------15FB59E21CFB-- From bear@ellington.Pharmacy.arizona.edu Wed May 13 13:30:44 1998 Received: from ellington.Pharmacy.arizona.edu for bear@ellington.Pharmacy.arizona.edu by www.ccl.net (8.8.3/950822.1) id NAA04063; Wed, 13 May 1998 13:19:32 -0400 (EDT) Received: (from bear@localhost) by ellington.Pharmacy.arizona.edu (8.8.5/8.8.5) id KAA11408 for chemistry@www.ccl.net; Wed, 13 May 1998 10:19:33 -0700 (MST) Date: Wed, 13 May 1998 10:19:33 -0700 (MST) From: Soaring Bear Message-Id: <199805131719.KAA11408@ellington.Pharmacy.arizona.edu> To: chemistry@www.ccl.net Subject: CCL:low barrier hydrogen bonds >low barrier hydrogen bonds (LBHB for short) >... >I was wondering if anyone could tell me whether >the common molecular mechanics force fields could be expected to properly >model LBHB. Can one expect AMBER, CHARMm, etc., to accurately predict the >LBHB lengths and frequencies? Or are these bonds unusual enough that new >terms need to be included? Considering how variable crystal hydrogen bonds are [see Gilli in "Fund Princ of Molec Modeling" ed W Gans 1996 and GA Jeffrey & W Saenger "Hydrogen Bonding in Biol. Structures" 1991] modeling forcefields can only be expected to be an approximation. SOARING BEAR PhD bear@pharmacy.arizona.edu Computational Medicinal Chemistry; Molecular Modeling; Pharmacognosy Protein & DNA Structural Biology; Cancer Biochemistry; Informatics; QSAR http://ellington.pharmacy.arizona.edu/~bear/resume.html currently seeking employment From bear@ellington.Pharmacy.arizona.edu Wed May 13 14:30:44 1998 Received: from ellington.Pharmacy.arizona.edu for bear@ellington.Pharmacy.arizona.edu by www.ccl.net (8.8.3/950822.1) id NAA04110; Wed, 13 May 1998 13:31:19 -0400 (EDT) Received: (from bear@localhost) by ellington.Pharmacy.arizona.edu (8.8.5/8.8.5) id KAA11441 for chemistry@www.ccl.net; Wed, 13 May 1998 10:31:21 -0700 (MST) Date: Wed, 13 May 1998 10:31:21 -0700 (MST) From: Soaring Bear Message-Id: <199805131731.KAA11441@ellington.Pharmacy.arizona.edu> To: chemistry@www.ccl.net Subject: CCL:Database Search >I'm looking for a database or a compatible combination of databases check the properties section of my chem web page at: http://ellington.pharmacy.arizona.edu/~bear/chem.html SOARING BEAR PhD bear@pharmacy.arizona.edu Computational Medicinal Chemistry; Molecular Modeling; Pharmacognosy Protein & DNA Structural Biology; Cancer Biochemistry; Informatics; QSAR http://ellington.pharmacy.arizona.edu/~bear/resume.html currently seeking employment From rschmid@acs.ucalgary.ca Tue May 12 21:30:37 1998 Received: from ds11.acs.ucalgary.ca for rschmid@acs.ucalgary.ca by www.ccl.net (8.8.3/950822.1) id UAA29879; Tue, 12 May 1998 20:43:01 -0400 (EDT) Received: from localhost by acs1.acs.ucalgary.ca (AIX 4.1/UCB 5.64/4.03) id AA51334; Tue, 12 May 1998 18:41:37 -0600 Date: Tue, 12 May 1998 18:41:36 -0600 (MDT) From: Rochus Schmid To: ccl Subject: molecular builder Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, Please forgive me for asking that question, which came up a couple of times already, I know. But I am desperate and my question is rather specific: I am searching for a (simple!!!, 3D!) molecular builder: - it should run under UNIX/X and be free (I know cerius2 and insightII and and and ....) - it should be very simple (I don't need ruberbands, rayshading etc. and it is only for a couple of atoms and not for proteins) - it should be able to add or delete atoms by mouse and change bond length, angles and dihedrals by selecting the atoms. - it should be able to read and write the stuff as pdb or xyz or whatever I follow this mailing list for quite a while now and similar questions came up quite often, I know. So I know about gopenmol and xmol and viewmol and molden and vmd and a couple more. But none of these programs is what I'm looking for. To make that more clear: I really like xmol. It's simple and free etc. but you can't build molecules. And I really liked the UNICHEM interface by Cray. This was perfect to me but it is not free ;-) Is there anything on this beautifull world like that?? I can't believe, that I'm the only one who needs that kind of software. Thanks in advance for any comment or hint. Happy computing, Rochus ******************************************************************** Rochus Schmid Phone: (403) 220-3232 University of Calgary Fax: (403) 289-9488 Department of Chemistry Email: rschmid@acs.ucalgary.ca 2500 University Drive N.W. Calgary, Alberta Canada T2N 1N4 http://www.chem.ucalgary.ca/groups/ziegler/ ******************************************************************** From krys.radacki@ac.rwth-aachen.de Thu May 14 16:31:00 1998 Received: from mail.rwth-aachen.de for krys.radacki@ac.rwth-aachen.de by www.ccl.net (8.8.3/950822.1) id PAA12374; Thu, 14 May 1998 15:54:05 -0400 (EDT) Received: from ac.rwth-aachen.de (pae102.ac.RWTH-Aachen.DE) by mail.rwth-aachen.de (PMDF V5.1-10 #23726) with ESMTP id <01IX0V1BB8SU000051@mail.rwth-aachen.de> for chemistry@www.ccl.net; Thu, 14 May 1998 12:28:03 +0200 Date: Thu, 14 May 1998 10:27:04 +0000 From: Krzysztof Radacki Subject: gaussview error by IRC Sender: root@mail.rwth-aachen.de To: Comutating Chemistry List Message-id: <355AC6F8.46B245C2@ac.rwth-aachen.de> Organization: Inst. Inorg. Chem., RWTH Aachen, Germany MIME-version: 1.0 X-Mailer: Mozilla 4.05 [en] (X11; I; Linux 2.1.99 i586) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit Excuse me, but again GaussView. I've done some IRC calculation what I can see in *.log is Normal termination of Gaussian 94. What I can see when I try to see it in GaussView is error dialog: "This <.log> file does not contain an Archive Entry. "Readin the last available Geometry instead. This I can understand because there is realy no archive entry.The next dialog is "Filename: "/.tmp.../kr003-IRC.log " "Activietes: " -Reading Gaussian Out file " -Parsing Gaussian LOG file " -Reading Gaussian Charge Data " "Error Message: " Invalid Charge Data (Line 2183) Any sugestions? By the way only one answer I've become on my last question was useing molden instead of gaussview. regards Krzys Radacki _________________________---------------------------------------------------- ------------------------- e-mail: Krys.Radacki@ac.RWTH-Aachen.DE --- ----------------------------------------------------------------------------- From lim@deakin.edu.au Thu May 14 20:31:02 1998 Received: from hestia.its.deakin.edu.au for lim@deakin.edu.au by www.ccl.net (8.8.3/950822.1) id UAA13132; Thu, 14 May 1998 20:02:43 -0400 (EDT) Received: from [128.184.88.60] (ara10.bcs.deakin.edu.au [128.184.88.60]) by hestia.its.deakin.edu.au (8.8.8/8.8.8) with ESMTP id KAA22347 for ; Fri, 15 May 1998 10:02:30 +1000 (EST) X-Sender: lim@128.184.136.2 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 15 May 1998 10:04:08 +1000 To: chemistry@www.ccl.net From: "Kieran F Lim (Lim Pak Kwan)" Subject: nmr prediction Can you recommend some good references (and software!) for calculating C-13 nmr spectra. thank you Kieran ------------------------------------------------------------ Dr Kieran F Lim Biol. and Chemical Sciences (Lim Pak Kwan) Deakin University ph: + [61] (3) 5227-2146 Geelong VIC 3217 fax: + [61] (3) 5227-1040 AUSTRALIA mailto:lim@deakin.edu.au http://www.deakin.edu.au/~lim