From hebant@ext.jussieu.fr Tue Jun 11 04:53:05 1996 Received: from shiva.jussieu.fr for hebant@ext.jussieu.fr by www.ccl.net (8.7.5/950822.1) id EAA16807; Tue, 11 Jun 1996 04:17:14 -0400 (EDT) Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.7.5/jtpda-5.2) with ESMTP id KAA03117 for ; Tue, 11 Jun 1996 10:17:14 +0200 (METDST) Received: from [134.157.11.16] by idf.ext.jussieu.fr (8.6.10/jtpda-4.0) with SMTP; Tue, 11 Jun 1996 10:17:10 +0200 X-Sender: hebant@idf.ext.jussieu.fr Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 11 Jun 1996 10:18:41 +0100 To: CHEMISTRY@www.ccl.net From: hebant@ext.jussieu.fr (Pascal HEBANT) Subject: NMR shielding calculations Hi all, I am performing NMR shielding calculations (of 7Li) but it seems to me that the results are very dependant of the molecular geometry and that a small change in the structure induces important changes for the chemical shift. Have you more informations about this assumption? More generally, what is the accuracy of such calculations? Regards ***************************************************************************** Pascal HEBANT Laboratoire d'Electrochimie et de Chimie Analytique Ecole Nationale Superieure de Chimie de Paris 11 rue Pierre et Marie Curie 75005 Paris FRANCE tel: 33 (1) 44 27 66 94 fax: 33 (1) 44 27 67 50 http://alcyone.enscp.jussieu.fr/Pages/LECA/Electrochimie.html ***************************************************************************** From smori@utsc.s.u-tokyo.ac.jp Tue Jun 11 06:53:11 1996 Received: from utsc.s.u-tokyo.ac.jp for smori@utsc.s.u-tokyo.ac.jp by www.ccl.net (8.7.5/950822.1) id GAA17502; Tue, 11 Jun 1996 06:19:08 -0400 (EDT) Received: by utsc.s.u-tokyo.ac.jp (8.7.5+2.6Wbeta6/TISN-1.3/R2) id TAA04087; Tue, 11 Jun 1996 19:18:51 +0900 (JST) Date: Tue, 11 Jun 1996 19:18:51 +0900 (JST) From: Seiji Mori Message-Id: <199606111018.TAA04087@utsc.s.u-tokyo.ac.jp> To: chemistry@www.ccl.net Subject: Contour map of Laplacian of raw Dear netters, I would like to draw the contour map in Laplacian of density with AIMPAC program which Prof.Bader developped. We can see recently many plotsof this type in papers. I do not know ,however, what plotting programs they use and recommend. Would you please tell me what program is easily and non-costly useful to plot contour map of Laplacian of the charge density and if you have or know, how should I get ? Macintosh program is the most appropriate for me , IBM-AIX ver.3 or SGI IRIX formatted programs are also suitable. Seiji Mori #################################################### Seiji Mori Graduate student Lab. of Physical Organic Chemistry Department of Chemistry The University of Tokyo Hongo 7-3-1, Bunkyou-ku, Tokyo 113, JAPAN. email:smori@utsc.s.u-tokyo.ac.jp --- http://www.chem.s.u-tokyo.ac.jp/Students/smori.html #################################################### From ANDRUNIO@Trurl.ch.uj.edu.pl Tue Jun 11 07:13:28 1996 Received: from nms.cyf-kr.edu.pl for ANDRUNIO@Trurl.ch.uj.edu.pl by www.ccl.net (8.7.5/950822.1) id GAA17406; Tue, 11 Jun 1996 06:05:13 -0400 (EDT) Received: from Trurl.ch.uj.edu.pl (trurl.ch.uj.edu.pl [149.156.72.6]) by nms.cyf-kr.edu.pl (8.6.11/8.6.11) with ESMTP id LAA10891 for ; Tue, 11 Jun 1996 11:27:27 +0200 Received: from TRURL/MAILQUEUE by Trurl.ch.uj.edu.pl (Mercury 1.21); 11 Jun 96 11:20:04 GMT+2 Received: from MAILQUEUE by TRURL (Mercury 1.21); 11 Jun 96 11:19:42 GMT+2 From: "Tadeusz Andruniow" Organization: Faculty of Chemistry, UJ To: chemistry@www.ccl.net Date: Tue, 11 Jun 1996 11:19:39 MET+2 X-pmuue: Q X-finfo: DOS,"Q",,,,Unknown Subject: g94 Priority: normal X-mailer: Pegasus Mail v3.22 Message-ID: <73F3497F24@Trurl.ch.uj.edu.pl> * This message contains the file 'Q', which has been * uuencoded. If you are using Pegasus Mail, then you can use * the browser's eXtract function to lift the original contents * out to a file, otherwise you will have to extract the message * and uudecode it manually. begin 660 Q M($1E87(@3F5T=&5R6QE;B!I;B!A(&)I9R!B87-I M&5P="!B87-I2!S=')A;F=E(&UE2!G("`@("`@("`@("!4861E=7-Z($%N9')U;FEO=PT* end From owner-chemistry@ccl.net Tue Jun 11 09:53:15 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id JAA18161; Tue, 11 Jun 1996 09:51:12 -0400 (EDT) Received: from s151h14.rega.kuleuven.ac.be for hans@s151h14.rega.kuleuven.ac.be by bedrock.ccl.net (8.7.5/950822.1) id JAA01288; Tue, 11 Jun 1996 09:51:09 -0400 (EDT) Received: by s151h14.rega.kuleuven.ac.be (950413.SGI.8.6.12/950213.SGI.AUTOCF) for chemistry@ccl.net id PAA01539; Tue, 11 Jun 1996 15:51:21 +0200 From: "Hans De Winter" Message-Id: <9606111551.ZM1537@s151h14.rega.kuleuven.ac.be> Date: Tue, 11 Jun 1996 15:51:04 -0600 X-Mailer: Z-Mail (3.2.1 6apr95 MediaMail) To: chemistry@ccl.net Subject: Summary: Software for DNA helix analysis Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi All:- About a week ago I posted a question regarding software for the analysis of oligonucleotide structure in terms of twist, roll, and so on. Here is a summary of replies (shortened). Thanks to all who replied. Hans De Winter **************************************************************************** NEWHELIX: It can be found on our departmental server at www.mbi.ucla.edu. Ho Leung Ng (ng@tesla.mbi.ucla.edu) **************************************************************************** You might like to see the helix computational methods in : Computers and Chemistry, (1996) vol. 20, pp. 339-345. James Crabbe (m.j.c.crabbe@rdg.ac.uk) **************************************************************************** Richard Lavery and Heinz Sklenar have written a very useful nucleic acid helical analysis program called CURVES. I think the current version is CURVES 4.1 and its available free directly from the author: | Richard Lavery | Tel : +33 1 43 25 26 09 | | Laboratoire de Biochimie Theorique | Fax : +33 1 43 29 56 45 | | Institut de Biologie Physico-Chimique | | | 13, rue Pierre et Marie Curie | Email: richard@ibpc.fr | | 75005 Paris, France | | Alexander Hillisch (hillisch@imb-jena.de) **************************************************************************** Hei Hans, I use a program called CURVES for this purpose. CURVES allows (optional) a bending of the helix axis whereas NEWHELIX only handles a rigid helix axis. But the differences for roll, twist etc. are small. CURVES is available from Richard Lavery in Paris. Newhelix is now available within Insight from Biosym/MSI. Hope it helps, Peter (slickers@imb-jena.de) **************************************************************************** Please contact either Prof. Wilma Olson at olson@chemf.rutgers.edu or Dr. Marla Babcock at marla@chemf.rutgers.edu. They have a program (the name of which escapes me at the moment) which is superior to NEWHELIX. References for their program are: J. Biomol. Struc. Dyn. vol 11, no.3 pp 597-628 (1993) J. Mol. Biol. vol 237, pp 98-124 (1994) J. Mol. Biol. vol 237, pp 125-156 (1994) Jeff Nauss (Jeffrey.Nauss@UC.Edu) **************************************************************************** See amber41/Questions/0Net/programs.anal or the same file under 'info from the net' on our web site http://www.amber.ucsf.edu/amber/ Bill Ross (ross@cgl.ucsf.EDU) From topper@cooper.edu Tue Jun 11 10:53:08 1996 Received: from magnum.cooper.edu for topper@cooper.edu by www.ccl.net (8.7.5/950822.1) id JAA18245; Tue, 11 Jun 1996 09:55:01 -0400 (EDT) Received: from zeus.cooper.edu by magnum.cooper.edu with SMTP id AA24184 (5.65c/IDA-1.4.4 for ); Tue, 11 Jun 1996 09:57:12 -0400 Received: by zeus.cooper.edu id AA05151 (5.67b/IDA-1.5); Tue, 11 Jun 1996 09:53:50 -0400 From: TOPPER ROBERT Message-Id: <199606111353.AA05151@zeus.cooper.edu> Subject: Re: CCL:Monter Carlo applications to diffusion? To: Andrey.Bliznyuk@anu.edu.au Date: Tue, 11 Jun 1996 09:53:50 -0400 (EDT) Cc: chemistry@www.ccl.net In-Reply-To: <199606110134.LAA06248@anugpo.anu.edu.au> from "Andrey Blizniuk" at Jun 11, 96 10:57:21 am X-Mailer: ELM [version 2.4 PL24alpha3] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit > > I am looking for application of Monter Carlo methods to > the diffusion problem. Any references are welcome. It seems, people > prefer to use Brownian dynamics (any ideas why?). > > Thanks, > > Dr. Andrey Bliznyuk > Computational Molecular Biology and Drug Design Group > Division of Molecular Biology and Biochemistry > John Curtin School of Medical Research > Australian National University > PO Box 334, Canberra, ACT 2601 > Australia > Email: Andrey.Bliznyuk@anu.edu.au > http://biocomp.anu.edu.au/~aab > Andrey, some of the links on the Molecular Monte Carlo Home Page may help. Have a look at http://www.cooper.edu/engineering/chemechem/monte.html best, robert ************************************************************************ Robert Q. Topper email: topper@cooper.edu Asst. Prof. of Chemistry phone: (212) 353-4378 The Cooper Union FAX: (212) 353-4341 51 Astor Place subway: take the 6 to Astor Place New York, NY 10003 USA or the N/R to 8th St/NYU http://www.cooper.edu/engineering/chemechem/depts_info/topper.html ************************************************************************ From suleyman@ccwf.cc.utexas.edu Tue Jun 11 14:57:06 1996 Received: from piglet.cc.utexas.edu for suleyman@ccwf.cc.utexas.edu by www.ccl.net (8.7.5/950822.1) id OAA21187; Tue, 11 Jun 1996 14:16:14 -0400 (EDT) Received: (from suleyman@localhost) by piglet.cc.utexas.edu (8.7.5/8.7.3/piglet.mc-1.4) id NAA25998; Tue, 11 Jun 1996 13:16:06 -0500 (CDT) Date: Tue, 11 Jun 1996 13:16:06 -0500 (CDT) From: Suleyman Bahceci X-Sender: suleyman@piglet.cc.utexas.edu To: CHEMISTRY@www.ccl.net Subject: Matrices-comparision program Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, I have a problem in which I need to compare matrices ( matrix superposition), that is, to find out all the matrix elements which have the same value (within a certain limit) in to or several matrices. I would be greatfull to anyone who can help me to find an appropriate program. If there is common interest, I will summarize the replies. Thanks in advances Suleyman <~><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><~> <|> Suleyman Bahceci <|> <|> The Unv. of Texas at Austin Tel: (512) 471-4671 (w) <|> <|> Dept. of Chemistry (512) 302-1791 (h) <|> <|> WEL 3.140 Email:suleyman@eeyore.cm.utexas.edu <|> <|> Austin, TX 78712 <|> <~><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><~> From orcaro@lux.levels.unisa.edu.au Tue Jun 11 21:53:30 1996 Received: from lux.levels.unisa.edu.au for orcaro@lux.levels.unisa.edu.au by www.ccl.net (8.7.5/950822.1) id VAA22966; Tue, 11 Jun 1996 21:11:33 -0400 (EDT) Received: by lux.levels.unisa.edu.au (5.x/SMI-SVR4) id AA10049; Wed, 12 Jun 1996 10:41:16 +0930 From: orcaro@lux.levels.unisa.edu.au (orcaro) Message-Id: <9606120111.AA10049@lux.levels.unisa.edu.au> Subject: MOPAC versions To: chemistry@www.ccl.net (Comp Chem List) Date: Wed, 12 Jun 1996 10:41:16 +0930 (GMT+0930) X-Mailer: ELM [version 2.4 PL25] Content-Type: text Hi all, We currently run MOPAC 93.00 on a general-purpose UNIX machine which every man and his dog also use. Consequently, it runs very slowly, particularly on the large systems we are examining. We would like to know if there are versions available for a) SGI Indy 200, or b) parallel processors, eg CM-5. Thanks for your help. * Anthony O'Dea * * orcaro@lux.levels.unisa.edu.au * * South Australian Surface Technology Centre * * Ian Wark Research Institute * * University of South Australia *