From KATEY@psipsy.uct.ac.za Mon Dec 5 02:17:21 1994 Received: from ucthpx.uct.ac.za for KATEY@psipsy.uct.ac.za by www.ccl.net (8.6.9/930601.1506) id CAA05774; Mon, 5 Dec 1994 02:01:15 -0500 Received: by ucthpx.uct.ac.za (/\==/\ Smail3.1.28.1 #28.43) id m0rEXPt-000KGHC; Mon, 5 Dec 94 09:00 SAST Received: From ITS/WORKQ1 by charongw1.uct.ac.za via Charon-4.0A-VROOM with IPX id 100.941205085801.480; 05 Dec 94 09:03:50 -0200 Message-ID: To: CHEMISTRY@ccl.net From: KATEY@psipsy.uct.ac.za Date: 5 Dec 94 09:01:09 SAST-2 Subject: macromodel question Priority: normal X-mailer: Pegasus Mail v2.3 (R4). I want to find out about purchasing a new version of Macromodel. Can anyone please supply me with the relevant email address or fax number. I would also like to find out how to go about subscribing to this group. Please send your reply to katey@psipsy.uct.ac.za. Thank you in advance for your help. Kate Sunter. From tomic@olimp.irb.hr Mon Dec 5 06:18:11 1994 Received: from olimp.irb.hr for tomic@olimp.irb.hr by www.ccl.net (8.6.9/930601.1506) id FAA07618; Mon, 5 Dec 1994 05:17:39 -0500 From: Received: by olimp.irb.hr (MX V4.1 VAX) id 21; Mon, 05 Dec 1994 11:17:23 MET-DST Date: Mon, 05 Dec 1994 11:17:23 MET-DST To: CHEMISTRY@ccl.net Message-ID: <009887BA.3DF12E68.21@olimp.irb.hr> Subject: Enrico Clementi Dear Netters, I would be grateful if somebody send me e-mail address of Enrico Clementi. Sanja e-mail: tomic@olimp.irb.hr From wurtz@conti.u-strasbg.fr Mon Dec 5 09:17:35 1994 Received: from conti.u-strasbg.fr for wurtz@conti.u-strasbg.fr by www.ccl.net (8.6.9/930601.1506) id IAA09773; Mon, 5 Dec 1994 08:51:19 -0500 From: Received: by conti.u-strasbg.fr; id AA22216; Mon, 5 Dec 1994 14:51:25 +0100 Message-Id: <9412051351.AA22216@conti.u-strasbg.fr> To: chemistry@ccl.net Cc: wurtz@conti.u-strasbg.fr Subject: Molecular Graphics Society Date: Mon, 05 Dec 94 14:51:25 +0100 X-Mts: smtp Dear netter, I would like to register as a member of the Molecular graphics society and also to subscribe to the Journal of Molecular Graphics. I have sent a mail at the following address : Dr. Rod Hubbard Department of Chemistry, University of Yprk Heslington, York, YO1 5DD, UK But I did not get an answer.Could somebody send me an e-mail or phone number. Thank you, Jean-Marie My address is the following : WURTZ Jean-Marie Laboratoire de Biologie Structurale IGBMC, CNRS 1, rue Laurent Fries 67404 ILLKIRCH-GRAFFENSTADEN, FRANCE Phone: 88 65 35 29 E-mail: wurtz@igbmc.u-strasbg.fr From schneid@tc.cornell.edu Mon Dec 5 09:25:55 1994 Received: from theory.tc.cornell.edu for schneid@tc.cornell.edu by www.ccl.net (8.6.9/930601.1506) id IAA09631; Mon, 5 Dec 1994 08:40:04 -0500 Received: from [128.84.162.55] (schneid.tc.cornell.edu [128.84.162.55]) by theory.tc.cornell.edu (8.6.9/8.6.6) with SMTP id IAA30520; Mon, 5 Dec 1994 08:39:53 -0500 X-Sender: schneid@theory.tc.cornell.edu Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 5 Dec 1994 08:34:56 -0500 To: "Sandra" , chemistry@ccl.net From: schneid@TC.Cornell.EDU (David J. Schneider) Subject: Re: CCL:EPR simulation software Cc: crepeau@msc.cornell.edu, dbudil@neu.edu Sandra, I have written some codes for slow-motional lineshape calculations which appeared in volume 8 of "Biological Magnetic Resonance". The first chapter in this volume describes the requisite aspects of the stochastic Liouville and contains a complete user's guide. Since 1989, these codes have been greatly extended by members of the Freed group, especially Dave Budil [now at Northeastern University]. Dave's email address is "dbudil@neu.edu". I suggest you contact him directly for more information. The appropriate contact in Freed's group is Dick Crepeau, "crepeau@msc.cornell.edu Dave At 1:39 PM 12/3/94, Sandra wrote: >Hallo, I'm a post-doc at the Chemistry Department of the University of >Florence. I'm insterested in having a survey on the available EPR software, >especially those programs dealing with ionic or nitroxide probes in >microscopically ordered and dispersed system. Thanks to all that will >give me some informations. > > >dr. Sandra Ristori >Laboratorio di Chimica Fisica dei Colloidi e delle Interfasi >Dipartimento di Chimica - Universita' degli Studi di Firenze >via Gino Capponi 9 >50121 Firenze ITALY >e-mail ristoris@mailserver.idg.fi.cnr.it > > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: ristoris@mailserver.idg.fi.cnr.it >-- Original Sender From: Address: ristoris@mailserver.idg.fi.cnr.it >CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator >MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 >Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search >http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV Dave Schneider 626 Engineering and Theory Center Cornell University Ithaca, NY 14853 Phone: (607) 254-4510 Fax: (607) 254-8888 Email: schneid@tc.cornell.edu From tore@physchem.kth.se Mon Dec 5 10:17:26 1994 Received: from link.physchem.kth.se for tore@physchem.kth.se by www.ccl.net (8.6.9/930601.1506) id JAA10818; Mon, 5 Dec 1994 09:50:14 -0500 Received: by physchem.kth.se (MX V4.0-1 VAX) id 5; Mon, 05 Dec 1994 15:50:43 EST Date: Mon, 05 Dec 1994 15:50:41 EST From: Tore Brinck To: CHEMISTRY@ccl.net Message-ID: <009887E0.6C2974E0.5@physchem.kth.se> Subject: vdW parameters for Cu(I) Dear Netters, I am looking for vdW parameters for Cu(I). These should preferably have been developed for the Amber FF, but other parameters of the Lennard-Jones type might work as well. Is there a straightforward method for calculating vdw parameters for transition metals using ab initio or DFT techniques? Thank you! Tore Brinck Dep. of Chemistry Royal Institute of Technology Stockholm, Sweden tore@physchem.kth.se From yuan@nka1.med.uc.edu Mon Dec 5 12:19:35 1994 Received: from nka1.med.uc.edu for yuan@nka1.med.uc.edu by www.ccl.net (8.6.9/930601.1506) id LAA13062; Mon, 5 Dec 1994 11:20:42 -0500 Received: by nka1.med.uc.edu (920330.SGI/921111.SGI.AUTO) for chemistry@ccl.net id AA16771; Mon, 5 Dec 94 11:20:42 -0500 Date: Mon, 5 Dec 1994 11:20:35 -0500 (EST) From: Jie Yuan To: Computational Chemistry List Subject: PDB search for Na or K ion containing molecules Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi CCLers: How can I search PDB or other data bases for molecules that contain certain metal ions (Na, K, Ca, etc.)? I have tried the Molecule R Us at NIH's WWW site, but could not get any hit. There is no way of searching the data files beyond the bibliographic header. Metal ions are heteroatoms. They are usually not mentioned in the header. It seems that the only way to search them is to scan the full files. We have the PDB CDROM so that a grep search on the files is possible. But I wish there are better ways and be able to access more databases. Thanks a lot for your attention! Jie -- Jie Yuan -- Pharmacology & Cell Biophysics -- U. Cincinnati -- == Phone: 513-558-2352 == Fax: x-1169 == Email: jie.yuan@uc.edu == == Mail: ML 0575, 231 Bethesda Ave., Cincinnati, OH 45267-0575 == From phys13@unix.york.ac.uk Mon Dec 5 12:23:59 1994 Received: from leeman.york.ac.uk for phys13@unix.york.ac.uk by www.ccl.net (8.6.9/930601.1506) id LAA13301; Mon, 5 Dec 1994 11:32:29 -0500 Received: from tower.york.ac.uk by leeman.york.ac.uk with SMTP (PP) id <16673-0@leeman.york.ac.uk>; Mon, 5 Dec 1994 14:59:32 +0000 Received: by tower.york.ac.uk (940715.SGI.52/931108.SGI.ANONFTP) for @leeman.york.ac.uk:chemistry@ccl.net id AA26111; Mon, 5 Dec 94 15:02:05 GMT Date: Mon, 5 Dec 1994 15:02:03 +0000 From: RJ Greenall X-Sender: phys13@tower.york.ac.uk To: chemistry@ccl.net Subject: SUMMARY: Animation on a 486 PC. Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Three people emailed wanting to see a summary, so here it is. Had to edit out a very long section on Hyperchem, ChemPlus and HyperNMR by Graham Hurst, but I'm sure he would forward you a version if you email him ( as well as .signatures etc ). Kept the price list for these products though, since this is usually a deciding factor in academia whether you will email him for more details ! Original post: > > > Hi, > > Is there any software (free or commercial) to > graphically demonstrate MD simulation on a 486 PC > which would impress school children and possibly persuade > them to take up courses in molecular biophysics/computational > chemistry ? > > Full MD facilities would be preferable, but packages > that could impressively animate say, amber trajectories, would > also be very useful. > > Thanks. > From: Bill Ross If you want to run Unix, mdxvu by Mark Forster (from QCPE) may do the trick. It reads amber trajectories anyway. He wrote "It has been accepted by QCPE (number 627 SGRW I think)" back in 1992 when he was about to go work at Biosym - maybe he's still there. Bill Ross ======================================== From: Jeffrey J Gosper I have recently written a program that runs under windows on a PC which can animate molecular phenomena such as reactions, vibrations, etc. At present my program does not read in AMBER trajectories directly however I am interesting in looking at the file format so that I could incorporate a conversion module. However, if you can generate a concatinated xyz format file then my program can read it in and animate it. The only other consideration is the size of the molecules you are interested in my program works very well with small molecules but it can handle (and produce) animation sequences for medium sized molecules. If your interest in my program please contact me directly and please send me information and a typical amber file so I can possible included the converter in my program. ======================================== From: Frits Daalmans If you put Linux on your PC, you will have all free UNIX MD codes available to you, and you can use X-windows. For more information: finger torvalds@klaava.helsinki.fi Linux is a GPL (Copyleft) UNIX clone, and is POSIX compliant. We are thinking of using it to teach 2nd year chemistry students MD and MM. Greetings, Frits ======================================== From: mirko@sara.nl Hello, Since I am Macintosh-based I don't have many info on 486-software, but when I started MM, I used PCModel (Serena Software) on PC and Mac. The graphics are not very beautiful, but you can see a molecule move and vibrate with every iteration (finding H-bonds for 2 formic acid molecules, etc.) Maybe it can be of help. Sincerely, Mirko Kranenburg ======================================== From: Jim_Bareman.XRCC@xerox.com HyperChem is probably ideal for these purposes... -Jim ======================================== From: Graham Hurst HyperChem can run and playback MD simulations. A relatively unique capability is the ability to do MD with quantum mechanical calculation of forces and energies so that reactions with bond forming and breaking can be simulated. Here's more info on HyperChem: The following includes a flyer describing HyperChem, feature summaries for HyperChem, ChemPlus and HyperNMR and a price list. The HyperChem free demo version is available in PKZIP format from www.ccl.net in pub/chemistry/software/MS-WINDOWS/hcdemo.zip and it can be downloaded via anonymous ftp using binary transfer mode. ***************************************************************** ( Extensive literature on products ... thought it was too much for the general chemistry list so deleted, I'm sure Graham Hurst would be glad to forward you a copy if you are interested. Thought I would include the price list though, since this it more vital on whether you may follow this product up ! ) ***************************************************************** Hypercube Inc. Scientific Software Suggested Retail Price List (Prices in US dollars) Item Code Description Commercial Govt. Price and Education Price =================================================================== Software for PC's. HCHEM4-WIN HyperChem Release 4 for Windows 1995 995 CPLUS1-WIN ChemPlus Release 1 for Windows 795 495 HNMR1-WIN HyperNMR Release 1 for Windows 995 695 ------------------------------------------------------------------- Network Licensing Prices for HyperChem HCHEM4-WIN1 Network HChem Rel. 4 for Windows 1995 995 (1 Licence) HCHEM4-WIN5 Network HChem Rel. 4 for Windows 7995 3995 (5 Licences) HCHEM4- Network HChem Rel. 4 for Windows 14000 7000 WIN10 (10 Licences) HCHEM4- Network HChem Rel. 4 for Windows 24000 12000 WIN25 (25 Licences) HCHEM4- Network HChem Rel. 4 for Windows 32000 16000 WIN50 (50 Licences) HCHEM4-WINA Network HChem Rel. 4 for Windows 50000 25000 (Unlimited) HCMAN-WIN Extra HyperChem Rel. 4 Manual 150 150 Set for Windows ------------------------------------------------------------------- Upgrade Prices for HyperChem HC4UP3-WIN HyperChem Rel. 3 to 4 Update 195 195 HC4UP2-WIN HyperChem Rel. 2 to 4 Update 495 495 HC4UPN-WIN Update of N Non-Networking to Free Free Networking HC4 with N licenses ------------------------------------------------------------------- UNIX computational modules HNEWT4-UN1 Molecular Mechanics Back End - 2000 1000 UNIX (1) HNEWT4-UNA Molecular Mechanics Back End - 5000 2500 UNIX (Site) HNDO4-UN1 Semi Empirical Back End - UNIX 2000 1000 (1) HNDO4-UNA Semi Empirical Back End - UNIX 5000 2500 (Site) ------------------------------------------------------------------- o All PC software comes on 1.44 Mb diskettes. o Shipping costs are not included in prices. Hypercube, Inc. 419 Phillip St., Waterloo, Ont. Canada, N2L 3X2 TEL: (800) 960-1871, (519) 725-4040 FAX: (519) 725-5193 Internet E-Mail: info@hyper.com Graham Hurst (hurst@hyper.com) ======================================== From: Lars Ojamae You may want to have a look at the molecular animation program "moviemol". It runs on PC's and on silicon graphics Indigo and IBM RISC/6000 workstations. More information and a shareware version can be obtained by anonymous ftp from chem-ftp.mps.ohio-state.edu. Best regards, Dr. Lars Ojamae Phone (614) 292-7806 From toukie@zui.unizh.ch Mon Dec 5 10:04:38 1994 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.9/930601.1506) id KAA11211; Mon, 5 Dec 1994 10:04:35 -0500 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA19646; Mon, 5 Dec 94 16:04:28 +0100 X-Nupop-Charset: British Date: Mon, 5 Dec 1994 15:58:04 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <57485.toukie@zui.unizh.ch> To: chemistry@ccl.net, toukie@zui.unizh.ch Subject: MOPAC for choosing reaxn mechs? Status: R Dear Colleagues; I am interested in a particular substitution reaction AX + Y -> AY + X It is likely that this reaction proceeds predominantly by either of two routes: a classical Sn2 Walden-type inversion reaction Y- + AX -> [Y-A-X]- -> AY + X- or via a single electron transfer type of substitution reaction AX + Y- -> AX.- + Y. AX.- + Y. -> A. + X:- A. + Y. -> AY >From the nature of the reactants and products, it seems likely that the re- action involves free radicals. HOWEVER, my question is: Is there a way of deciding which of the above two postulated mechanisms is _most likely_ to predominate using MOPAC 6.0? Are there components of the output from a MOPAC run that enable you to decide whether the reaction likely proceeds as a single electron transfer reaction or as a Walden inversion? I am able to draw Z-matrices for the reactant, product, and all of the postu- lated mechanistic intermediates. I would ask people who are knowledgable about using MOPAC for studying paths or mechanisms of chemical reactions to kindly contact me on the above matter and to advise me how to proceed. Specifics (e.g., keywords, useful components of the MOPAC output) would be most sincerely appreciated, as would relevant literature references. I thank all responders for generously sharing their information with me. Yours respectfully, (Dr.) S. Shapiro Institut fuer orale Mikrobiologie und allgemeine Immunologie Zentrum fuer Zahn-, Mund-, und Kieferheilkunde der Universitaet Zuerich Plattenstrasse 11 Postfach CH-8028 Zuerich, Switzerland Internet: toukie@zui.unizh.ch FAX-nr: ( ... + 1) 261'56'83