From dstern@orgchem.kth.se Mon Aug 15 03:32:36 1994 Received: from kth.se for dstern@orgchem.kth.se by www.ccl.net (8.6.9/930601.1506) id CAA26721; Mon, 15 Aug 1994 02:50:30 -0400 Received: from [130.237.54.159] (orgchem-mac19.orgchem.kth.se [130.237.54.159]) by kth.se (8.6.7/8.6.9) with SMTP id IAA24385 for ; Mon, 15 Aug 1994 08:55:51 +0200 Message-Id: <199408150655.IAA24385@kth.se> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 15 Aug 1994 08:57:11 +0100 To: CHEMISTRY@ccl.net From: dstern@orgchem.kth.se (David Stern) Subject: Se & Te Hi netters, I would appreciate any references regarding tellurium and selenium parameters for MM2 and MM3 calculations. Thanks in advance. David Stern -------------------------------------------------------- David Stern Department of Chemistry, Organic Chemistry, Royal Institute of Technology, S-100 44 Stockholm,Sweden fax: +46-8-791.23.33 INTERNET: dstern@orgchem.kth.se -------------------------------------------------------- From mdqac@cluster3.urz.uni-halle.de Mon Aug 15 09:33:12 1994 Received: from mlucom.urz.uni-halle.de for mdqac@cluster3.urz.uni-halle.de by www.ccl.net (8.6.9/930601.1506) id JAA01387; Mon, 15 Aug 1994 09:20:44 -0400 From: Received: from cluster3.urz.Uni-Halle.DE by mlucom.urz.uni-halle.de with SMTP (1.36.108.7/15.6) id AA23880; Mon, 15 Aug 1994 15:26:39 +0200 Posted-Date: Mon, 15 Aug 1994 15:23:03 +0200 Received-Date: Mon, 15 Aug 1994 15:26:39 +0200 Received: by cluster3.urz.uni-halle.de (AIX 3.2/UCB 5.64/4.03) id AA29431; Mon, 15 Aug 1994 15:23:03 +0200 Date: Mon, 15 Aug 1994 15:23:03 +0200 Message-Id: <9408151323.AA29431@cluster3.urz.uni-halle.de> To: chemistry@ccl.net Subject: Parallel versions of comp. software Dear CCL-members, our computational center at the university plans to buy new hardware (parallel systems). It want to know from the important users (like us - the comp. chem. group) what we require for hard- and especially for software. So I have the following question(s): 1. What would you prefer as parallel-hardware for computational questions (some workstation as cluster, shared memory systems, distributed memory systems, how many processors). We do peptide and protein modelling with force field methods. 2. Are there any parallelized versions of the following programs available: Gromos, Amber (I know one), MM2P/MM3, Yeti, Mopac, Gamess, Turbomole. 3. What hard- and software requirements does this versions need? Please send answers to schinke@mlubio4.biochemtech.uni-halle.de I will compile a list for the net, if there are answers. Thank you for the help, H. Schinke =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= =-= Heiko Schinke =-= =-= Martin-Luther-University, Dept. of Biochemistry/Biotechnology =-= =-= P. O. Box 8, D-06099 Halle/Saale, Germany =-= =-= =-= =-= Phone: ++49/345/617242 FAX: ++49/345/647161 =-= =-= =-= =-= E-Mail: schinke@mlubio4.biochemtech.uni-halle.de =-= =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From IRIKURA@ENH.NIST.GOV Mon Aug 15 10:32:39 1994 Received: from ENH.NIST.GOV for IRIKURA@ENH.NIST.GOV by www.ccl.net (8.6.9/930601.1506) id KAA02775; Mon, 15 Aug 1994 10:24:21 -0400 From: Received: from ENH.NIST.GOV by ENH.NIST.GOV (PMDF V4.2-13 #4653) id <01HFXNR8AI68002LT4@ENH.NIST.GOV>; Mon, 15 Aug 1994 10:28:25 EDT Date: Mon, 15 Aug 1994 10:28:25 -0400 (EDT) Subject: G92 mp2 freq calc using little disk To: chemistry@ccl.net Message-id: <01HFXNR8DZK2002LT4@ENH.NIST.GOV> X-PS-Qualifiers: /LEFT_MARGIN=6/SIZE=11 X-VMS-To: IN%"chemistry@ccl.net" X-VMS-Cc: IRIKURA MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT >>From: IN%"kongsian@nsrc.nus.sg" 14-AUG-1994 22:15:28.00 >>To: IN%"chemistry@ccl.net" >>CC: >>Subj: CCL:G92: Help with MP2 FREQ calc. >> >>Running MP2 FREQ calculation on an optimized geometry. >>156 basis functions. >>MAXDISK = 100 MW >>MP2=VERYSTINGY >> >>Problem: >>G92 tries to create a 400MW .rwf (3.2GB!) file and runs out of disk space. >>I have 2G available for temp files. >> Kong, I've had luck using the following: # mp2/basis freq=Numer SCF=Direct Using scf=direct cuts down the disk requirement because atomic ints aren't stored. (For 156 basis fuctions, it may also be faster than using an integral file.) Using freq=numer cuts down the disk requirement because only first derivatives are calculated analytically. Using freq=numer also slows the calculation considerably, but, unlike the analytic second derivative calculation, it can be restarted from the checkpoint file using freq=(numer,restart). If this still doesn't work, maybe specifying mp2=fulldirect in addition to freq=numer will do it. Good luck! Karl ---------------------------------------------- Dr. Karl Irikura Chemical Kinetics and Thermodynamics Division National Institute of Standards and Technology Gaithersburg, MD 20899 ---------------------------------------------- From ADAMSL@CSOVAX.PORTSMOUTH.AC.UK Mon Aug 15 11:33:36 1994 Received: from sun2.nsfnet-relay.ac.uk for ADAMSL@CSOVAX.PORTSMOUTH.AC.UK by www.ccl.net (8.6.9/930601.1506) id LAA03396; Mon, 15 Aug 1994 11:06:55 -0400 From: Message-Id: <199408151506.LAA03396@www.ccl.net> Via: uk.ac.portsmouth.csovax; Mon, 15 Aug 1994 16:11:54 +0100 Date: Mon, 15 Aug 94 16:10 GMT To: CHEMISTRY Subject: Modeling Fe-EDTA compounds I am interested in modeling a proposed DNA cleavage molecule, which includes Fe chelated to EDTA. Has anyone any experience in modeling this kind of system, particularly using Sybyl? Lesley Adams Centre for Molecular Design University of Portsmouth U.K. From carlos@extreme.bio.cornell.edu Mon Aug 15 11:35:22 1994 Received: from CORNELLC.cit.cornell.edu for carlos@extreme.bio.cornell.edu by www.ccl.net (8.6.9/930601.1506) id LAA03530; Mon, 15 Aug 1994 11:18:05 -0400 Received: from extreme.bio.cornell.edu by CORNELLC.cit.cornell.edu (IBM VM SMTP V2R2) with TCP; Mon, 15 Aug 94 11:22:14 EDT Received: by extreme.bio.cornell.edu (920330.SGI/921111.SGI) for @cornellc.cit.cornell.edu:chemistry@ccl.net id AA12651; Mon, 15 Aug 94 11:08:33 -0400 Date: Mon, 15 Aug 94 11:08:33 -0400 From: carlos@extreme.bio.cornell.edu (Carlos Faerman) Message-Id: <9408151508.AA12651@extreme.bio.cornell.edu> To: chemistry@ccl.net Subject: summary of replies on how to interface GRID to InsightII Cc: carlos@extreme.bio.cornell.edu, fora@biosym.com I wish to thank the persons who kindly answered my question! Carlos H. Faerman carlos@extreme.bio.cornell.edu Here is a summary of the original question and the answers I received ============================================================================== QUESTION: ******** >Does anyone have a working interface between GRID (Peter Goodford) and >InsightII (version 2.3) (Biosym)? >I have run GRIDI, which supposedly converts the results to a format >expected by InsightII but I have not been successful... >If someone has already modified GRIDI to carry this task successfully, please >let me know >Carlos H. Faerman >carlos@extreme.bio.cornell.edu ANSWERS: ******** We have had no problem running GRID as GRIDI and importing the GRID contour files into Insight II for visualization. When running GRIDI make sure that the GRID input file defines a contour output file with the extension "grd" which can be recognized by Insight II. ( KONT = contour.grd ) After running GRIDI, start InsightII and select the grid option from the row of buttons with pictures on them. Within the grid option select'get'. This should bring up a file list of all the *.grd files in your directory. After you have imported the GRIDI output file, you will need to set energy levels and colors for display. This is also under the grid option. Don't confuse the 'contour' menu option with the 'grid' option in Insight II. You need to use the grid option for importing GRIDI results. Send me an e-mail if you still have problems after reading this. Good Luck Gene Coats coatse@cmda.abbott.com +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Carlos, I have used the program GRIDI and there are two ways to use the output files. The first is to use the contour utility which comes with InsightII to prepare contour file that can then be read into InsightII using the contour get facility. This gives the contour line like pictures. The second involves using get grid command under the Ampac/mopac menus. This gives nice solid surfaces, but you need to know the level that you want to display as InightII can't seem to handle negative contours. Both ways are very memory intensive and I was able to crash InsightII fairly easily doing either method. If you need any more help, just e-mail me. Bye for now, Jeff. Jeff Dyason Phone: (61 3) 903-9559 Victorian College of Pharmacy Fax: (61 3 ) 903-9582 Monash University e-mail: jcd@vcp.monash.edu.au 381 Royal Parade, Parkville, Victoria, 3052 Australia From mccarthy@convx1.ccit.arizona.edu Mon Aug 15 13:35:15 1994 Received: from Arizona.EDU for mccarthy@convx1.ccit.arizona.edu by www.ccl.net (8.6.9/930601.1506) id MAA06049; Mon, 15 Aug 1994 12:48:03 -0400 Received: from convx1.ccit.arizona.edu by Arizona.EDU (PMDF V4.3-9 #2381) id <01HFXMZ5JLC0987JON@Arizona.EDU>; Mon, 15 Aug 1994 09:53:27 -0700 (MST) Received: from localhost by convx1.ccit.arizona.edu; Mon, 15 Aug 1994 09:49:20 -0700 Date: Mon, 15 Aug 1994 09:49:20 -0700 From: mccarthy@convx1.ccit.arizona.edu (William Mccarthy) Subject: Re: CCL:G92: Help with MP2 FREQ calc. To: chemistry@ccl.net, kongsian@nsrc.nus.sg Message-id: <199408151649.JAA29129@convx1.ccit.arizona.edu> MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT To help avoid disk use, you might try the keywords "scf=direct" (courtesy of Almloef, I believe) when using G9X. "Direct" refers to recomputation of two-electron integrals as needed. This strategy helps my calcs require less space. Good luck, Will McCarthy From asmithi@cix.compulink.co.uk Mon Aug 15 13:37:30 1994 Received: from cix.compulink.co.uk for asmithi@cix.compulink.co.uk by www.ccl.net (8.6.9/930601.1506) id MAA06096; Mon, 15 Aug 1994 12:50:56 -0400 Received: from gonzales.compulink.co.uk (gonzales.compulink.co.uk [192.188.69.4]) by cix.compulink.co.uk (8.6.9/8.6.9) id RAA18018 for CHEMISTRY@ccl.net; Mon, 15 Aug 1994 17:53:46 +0100 Date: Mon, 15 Aug 94 17:56 BST-1 From: asmithi@cix.compulink.co.uk (Andrew Smith) Subject: Thanks for advice To: CHEMISTRY@ccl.net Reply-To: asmithi@cix.compulink.co.uk Message-Id: Many thanks for all the advice posted here re low spec CC. I think I'll go for MOPAC for the present, as I am in the perennial state of having no money. If it all comes flooding back and I get involved in a bigger way, I'll go for something a little more 'fancy' (I saw a demo of HyperChem a few years ago, and was VERY impressed, but it's too much for my current machine!) Thanks again, Andrew Smith From chjaim@unix1.sncc.lsu.edu Mon Aug 15 15:32:49 1994 Received: from unix1.sncc.lsu.edu for chjaim@unix1.sncc.lsu.edu by www.ccl.net (8.6.9/930601.1506) id OAA08035; Mon, 15 Aug 1994 14:32:41 -0400 Received: by unix1.sncc.lsu.edu (AIX 3.2/UCB 5.64/4.03) id AA26043; Mon, 15 Aug 1994 13:38:10 -0500 Date: Mon, 15 Aug 1994 13:38:10 -0500 From: chjaim@unix1.sncc.lsu.edu (Jaime Combariza) Message-Id: <9408151838.AA26043@unix1.sncc.lsu.edu> To: CHEMISTRY@ccl.net Subject: Molcas-3 announcement Cc: chjaim@unix1.sncc.lsu.edu Does any body have a copy of the announcement of the new version of Molcas (Molcas-3, I believe)? if so, could you please mail it to me? I have tried e-mail in the past to Sweden but for some reason I do not get responses. Besides this is August and many people may be on vacation there! Many thanks. Jaime Combariza From daisy@clio.rz.uni-duesseldorf.de Mon Aug 15 15:35:37 1994 Received: from clio.rz.uni-duesseldorf.de for daisy@clio.rz.uni-duesseldorf.de by www.ccl.net (8.6.9/930601.1506) id OAA08604; Mon, 15 Aug 1994 14:56:25 -0400 Received: from localhost by clio.rz.uni-duesseldorf.de (8.6.4/11.0) id VAA09671; Mon, 15 Aug 1994 21:01:40 +0200 From: daisy@clio.rz.uni-duesseldorf.de (The Very Lovely Daisy) Message-Id: <199408151901.VAA09671@clio.rz.uni-duesseldorf.de> Subject: NMR-Simulation software To: chemistry@ccl.net Date: Mon, 15 Aug 1994 20:01:40 +0100 (WET) X-Mailer: ELM [version 2.4 PL21] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1326 Heinrich-Heine-University Duesseldorf Institut of Inorganic Chemistry Prof. Dr. G. Haegele Dipl. Chem. R. Spiske Dear Netters, today we installed our DSYMPC program package to our universities ftp server. It is a NMR-Simulation program for up to 8 single spins. anonymous ftp to: ftp.rz.uni-duesseldorf.de and change directory to: /pub/msdos/chemie and find the files: dsympc.zip the program dsympc.manual.hp_deskjet.zip a manual printfile to use with an HP Deskjet dsympc.manual.postscript.zip a manual printfile to use with a Postscript printer This program package can be used without any fee. If you used this program for your work we expect you to cite the following article in: Phosphorus, Sulfur and Silicon, 1993, Vol. 77, p. 262 Title: NMR SIMULATION AND ITERATION TOOLS FOR PCs Authors: G. Haegele, R. Spiske, H.W. Hoeffken, T. Lenzen, U. Weber, S. Goudetsidis have fun Robert ------------------------------------------------------------------------------ Robert Spiske // daisy@clio.rz.uni-duesseldorf.de ------------------------------------------------------------------------------ From h.rzepa@ic.ac.uk Mon Aug 15 15:37:48 1994 Received: from punch.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.9/930601.1506) id OAA08663; Mon, 15 Aug 1994 14:59:27 -0400 Received: from sg1.cc.ic.ac.uk by punch.ic.ac.uk with SMTP (PP) id <23781-0@punch.ic.ac.uk>; Mon, 15 Aug 1994 20:03:43 +0100 Received: from macb.ch by cscmgb.cc.ic.ac.uk (920330.SGI/4.0) id AA29078; Mon, 15 Aug 94 20:07:29 +0100 Message-Id: <9408151907.AA29078@cscmgb.cc.ic.ac.uk> X-Sender: rzepa@sg1.cc.ic.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 15 Aug 1994 20:04:41 +0100 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Rzepa,Henry) (Rzepa,Henry) Subject: GIC: Global Instructional Chemistry: http://www.ch.ic.ac.uk/GIC/ Do you have any interesting stories to tell about chemistry? Something you might use in your teaching, or as part of a lab? Interesting laboratory preparations, or spectral analyses? On-line manuals? Ever wondered where you could get material for a tutorial at a moments notice? Or that new lab course your chairman has told you to set up this fall? Over the years, I have accumulated various snippets; too short or to diverse to turn into a book, but perhaps useful to other instructors and students at both undergraduate and postgraduate level. The World-Wide-Web offers one mechanism whereby we can all share in this wisdom. To facilitate this, a "Global Instructional Chemistry" page has been set up. This contains at the moment six categories, varying in character, and difficulty, and each perhaps appealing to a different audience. They are intended as demonstrators. If you feel this "clearing house" of chemical memorabilia is useful, write and let me know. (put GIC in the subject field please!) Even better, if you just happen to have some material prepared for a course that you would not mind sharing with others, send me the "URL" if you have already converted it to HTML, (or a Microsoft rtf file if you are asking "what is HTML?") and we will consider including it on the GIC page (we have to reserve the right not to include of course). Rtf should travel well across network, just "include" it as a document with your mailer. The Future? Well, if each chemistry faculty in the world created just ONE contribution, a "global chemistry academy" could be created! Does this do us all out of a job? Far from it! This stuff still has to be explained,examined and "evangelised" by real people to real people. It just makes us all more efficient, and even dare I imply more "up-to-date" in our instructional chemistry. Clearly if more material comes in, "editorialising" and organising will have to be applied. We also recognise that each department has its own style and content. This is not meant to replace that, merely to provide a mechanism where useful chemical information can be exchanged and acquired. To view the existing material connect to the URL http://www.ch.ic.ac.uk/GIC/ (or if that does not work) http://www.ch.ic.ac.uk/GIC/.index.html The intention is that this information be free, ie freely donated, and free to all. In due time, it could be pressed onto CD-ROM as a distribution method, but lets leave that for the future. Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 2.03, Tel (44) 171 594 5774 or 594 5809. Fax: (44) 171 594 5804 World-Wide-Web URL: http://www.ch.ic.ac.uk/rzepa.html From rgab@trpntech.com Mon Aug 15 16:32:47 1994 Received: from netcomsv.netcom.com for rgab@trpntech.com by www.ccl.net (8.6.9/930601.1506) id QAA10153; Mon, 15 Aug 1994 16:01:53 -0400 Received: from trpntech.com by netcomsv.netcom.com with UUCP (8.6.4/SMI-4.1) id MAA21568; Mon, 15 Aug 1994 12:59:34 -0700 Message-Id: <199408151959.MAA21568@netcomsv.netcom.com> Date: 15 Aug 1994 12:41:05 -0800 From: "Richard Bone" Subject: Intramolecular H-bonds- mor To: "CCL" Subject: Intramolecular H-bonds: more refs Further to the message I posted last week: 3 papers which address specifically the location and analysis of intramolecular interactions involving Hydrogen: J. Cioslowski, S. T. Mixon and W. D. Edwards, J. Am. Chem. Soc., 113, 1083, (1991) J. Cioslowski and S. T. Mixon, ibid, 114, (1992) J. Cioslowski and S. T. Mixon, Can. J. Chem., 70, 443, (1992) All employ Bader's Theory of Atoms in Molecules Richard Bone __________________________________________________________ Richard G. A. Bone, PhD. Computational Chemist Terrapin Technologies, Inc. South San Francisco USA E-mail rgab@trpntech.com From d3g359@rahman.pnl.gov Mon Aug 15 20:32:45 1994 Received: from pnl.gov for d3g359@rahman.pnl.gov by www.ccl.net (8.6.9/930601.1506) id UAA15090; Mon, 15 Aug 1994 20:15:08 -0400 From: Received: from carbon.pnl.gov by pnl.gov (PMDF V4.2-15 #4032) id <01HFY2GDBTHS003J56@pnl.gov>; Mon, 15 Aug 1994 17:16:25 PDT Received: from pnlg.pnl.gov by carbon.pnl.gov (4.1/SMI-4.1) id AA26461; Mon, 15 Aug 94 17:20:28 PDT Received: from rahman.pnl.gov (130.20.182.20) by pnlg.pnl.gov; Mon, 15 Aug 94 17:13 PDT Received: by rahman.pnl.gov (931110.SGI/920502.SGI) for @carbon.pnl.gov:CHEMISTRY@ccl.net id AA20159; Mon, 15 Aug 94 17:13:05 -0700 Date: Mon, 15 Aug 1994 17:13:05 -0700 Subject: g92 To: CHEMISTRY@ccl.net Message-id: <9408160013.AA20159@rahman.pnl.gov> Content-transfer-encoding: 7BIT Hi, I'd like to talk to anyone who has run gaussian92 on the SGI IP21 (R8000) chip. Thanks, John ------------------------------------------------------------------------------ John Nicholas Office: (509) 375-6559 Senior Research Scientist FAX: (509) 375-6631 Molecular Science Research Center Pacific Northwest Laboratory Mailstop K1-90 Richland, WA 99352 ------------------------------------------------------------------------------